function_id_one,function_one,function_id_two,function_two,functionality_type,big_clone_types,is_clone
1184290,"@Override
public void execute () {
    File currentModelDirectory = new File (this.globalData.getData (String.class, GlobalData.MODEL_INSTALL_DIRECTORY));
    File mobileDirectory = new File (currentModelDirectory, ""mobile"");
    mobileDirectory.mkdir ();
    File mobileModelFile = new File (mobileDirectory, ""mobile_model.zip"");
    FileOutputStream outputStream = null;
    ZipOutputStream zipStream = null;
    BusinessModel businessModel = BusinessUnit.getInstance ().getBusinessModel ();
    try {
        mobileModelFile.createNewFile ();
        outputStream = new FileOutputStream (mobileModelFile);
        zipStream = new ZipOutputStream (outputStream);
        Dictionary dictionary = businessModel.getDictionary ();
        for (Definition definition : dictionary.getAllDefinitions ()) {
            ZipEntry entry = new ZipEntry (definition.getRelativeFileName ());
            zipStream.putNextEntry (entry);
            writeBinary (definition.getAbsoluteFileName (), zipStream);
        }
        final String modelFilename = ""model.xml"";
        ZipEntry entry = new ZipEntry (modelFilename);
        zipStream.putNextEntry (entry);
        writeBinary (businessModel.getAbsoluteFilename (modelFilename), zipStream);
        final String logoFilename = dictionary.getModel ().getImageSource (LogoType.mobile);
        entry = new ZipEntry (logoFilename);
        zipStream.putNextEntry (entry);
        writeBinary (businessModel.getAbsoluteFilename (logoFilename), zipStream);
    } catch (IOException e) {
        agentLogger.error (e);
    } finally {
        StreamHelper.close (zipStream);
        StreamHelper.close (outputStream);
    }
}
",23247094,"void copyZipToZip (ZipInputStream zis, ZipOutputStream zos) throws Exception {
    ZipEntry entry;
    byte [] buffer = new byte [1];
    while ((entry = zis.getNextEntry ()) != null) {
        zos.putNextEntry (new ZipEntry (entry.getName ()));
        while (zis.available () == 1) {
            zis.read (buffer, 0, buffer.length);
            zos.write (buffer, 0, buffer.length);
        }
        zis.closeEntry ();
        zos.closeEntry ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
3596849,"private static void solve_l1r_l2_svc (Problem prob_col, double [] w, double eps, double Cp, double Cn) {
    int l = prob_col.l;
    int w_size = prob_col.n;
    int j, s, iter = 0;
    int max_iter = 1000;
    int active_size = w_size;
    int max_num_linesearch = 20;
    double sigma = 0.01;
    double d, G_loss, G, H;
    double Gmax_old = Double.POSITIVE_INFINITY;
    double Gmax_new;
    double Gmax_init = 0;
    double d_old, d_diff;
    double loss_old = 0;
    double loss_new;
    double appxcond, cond;
    int [] index = new int [w_size];
    byte [] y = new byte [l];
    double [] b = new double [l];
    double [] xj_sq = new double [w_size];
    double [] C = new double [] {Cn, 0, Cp};
    for (j = 0; j < l; j ++) {
        b [j] = 1;
        if (prob_col.y [j] > 0) y [j] = 1;
        else y [j] = - 1;

    }
    for (j = 0; j < w_size; j ++) {
        w [j] = 0;
        index [j] = j;
        xj_sq [j] = 0;
        for (FeatureNode xi : prob_col.x [j]) {
            int ind = xi.index - 1;
            double val = xi.value;
            xi.value *= y [ind];
            xj_sq [j] += C [GETI (y, ind)] * val * val;
        }
    }
    while (iter < max_iter) {
        Gmax_new = 0;
        for (j = 0; j < active_size; j ++) {
            int i = j + random.nextInt (active_size - j);
            swap (index, i, j);
        }
        for (s = 0; s < active_size; s ++) {
            j = index [s];
            G_loss = 0;
            H = 0;
            for (FeatureNode xi : prob_col.x [j]) {
                int ind = xi.index - 1;
                if (b [ind] > 0) {
                    double val = xi.value;
                    double tmp = C [GETI (y, ind)] * val;
                    G_loss -= tmp * b [ind];
                    H += tmp * val;
                }
            }
            G_loss *= 2;
            G = G_loss;
            H *= 2;
            H = Math.max (H, 1e-12);
            double Gp = G + 1;
            double Gn = G - 1;
            double violation = 0;
            if (w [j] == 0) {
                if (Gp < 0) violation = - Gp;
                else if (Gn > 0) violation = Gn;
                else if (Gp > Gmax_old / l && Gn < - Gmax_old / l) {
                    active_size --;
                    swap (index, s, active_size);
                    s --;
                    continue;
                }

            } else if (w [j] > 0) violation = Math.abs (Gp);
            else violation = Math.abs (Gn);

            Gmax_new = Math.max (Gmax_new, violation);
            if (Gp <= H * w [j]) d = - Gp / H;
            else if (Gn >= H * w [j]) d = - Gn / H;
            else d = - w [j];

            if (Math.abs (d) < 1.0e-12) continue;

            double delta = Math.abs (w [j] + d) - Math.abs (w [j]) + G * d;
            d_old = 0;
            int num_linesearch;
            for (num_linesearch = 0; num_linesearch < max_num_linesearch; num_linesearch ++) {
                d_diff = d_old - d;
                cond = Math.abs (w [j] + d) - Math.abs (w [j]) - sigma * delta;
                appxcond = xj_sq [j] * d * d + G_loss * d + cond;
                if (appxcond <= 0) {
                    for (FeatureNode x : prob_col.x [j]) {
                        b [x.index - 1] += d_diff * x.value;
                    }
                    break;
                }
                if (num_linesearch == 0) {
                    loss_old = 0;
                    loss_new = 0;
                    for (FeatureNode x : prob_col.x [j]) {
                        int ind = x.index - 1;
                        if (b [ind] > 0) {
                            loss_old += C [GETI (y, ind)] * b [ind] * b [ind];
                        }
                        double b_new = b [ind] + d_diff * x.value;
                        b [ind] = b_new;
                        if (b_new > 0) {
                            loss_new += C [GETI (y, ind)] * b_new * b_new;
                        }
                    }
                } else {
                    loss_new = 0;
                    for (FeatureNode x : prob_col.x [j]) {
                        int ind = x.index - 1;
                        double b_new = b [ind] + d_diff * x.value;
                        b [ind] = b_new;
                        if (b_new > 0) {
                            loss_new += C [GETI (y, ind)] * b_new * b_new;
                        }
                    }
                }
                cond = cond + loss_new - loss_old;
                if (cond <= 0) break;
                else {
                    d_old = d;
                    d *= 0.5;
                    delta *= 0.5;
                }
            }
            w [j] += d;
            if (num_linesearch >= max_num_linesearch) {
                info (""#"");
                for (int i = 0;
                i < l; i ++) b [i] = 1;

                for (int i = 0;
                i < w_size; i ++) {
                    if (w [i] == 0) continue;

                    for (FeatureNode x : prob_col.x [i]) {
                        b [x.index - 1] -= w [i] * x.value;
                    }
                }
            }
        }
        if (iter == 0) Gmax_init = Gmax_new;

        iter ++;
        if (iter % 10 == 0) info (""."");

        if (Gmax_new <= eps * Gmax_init) {
            if (active_size == w_size) break;
            else {
                active_size = w_size;
                info (""*"");
                Gmax_old = Double.POSITIVE_INFINITY;
                continue;
            }
        }
        Gmax_old = Gmax_new;
    }
    info (""%noptimization finished, #iter = %d%n"", iter);
    if (iter >= max_iter) info (""%nWARNING: reaching max number of iterations%n"");

    double v = 0;
    int nnz = 0;
    for (j = 0; j < w_size; j ++) {
        for (FeatureNode x : prob_col.x [j]) {
            x.value *= prob_col.y [x.index - 1];
        }
        if (w [j] != 0) {
            v += Math.abs (w [j]);
            nnz ++;
        }
    }
    for (j = 0; j < l; j ++) if (b [j] > 0) v += C [GETI (y, j)] * b [j] * b [j];

    info (""Objective value = %f%n"", v);
    info (""#nonzeros/#features = %d/%d%n"", nnz, w_size);
}
",8533735,"public void shuffle () {
    Card tempCard = new Card ();
    for (int i = 0;
    i < NUM_CARDS; i ++) {
        int j = i + r.nextInt (NUM_CARDS - i);
        tempCard = cards [j];
        cards [j] = cards [i];
        cards [i] = tempCard;
    }
    position = 0;
}
",Shuffle Array in Place,Type-3 (WT3/4),FALSE
469518,"public synchronized void writeFile (String filename) throws IOException {
    int amount;
    byte buffer [] = new byte [4096];
    File f = new File (filename);
    FileInputStream in = new FileInputStream (f);
    putNextEntry (new ZipEntry (f.getName ()));
    while ((amount = in.read (buffer)) != - 1) write (buffer, 0, amount);

    closeEntry ();
    in.close ();
}
",21524576,"private static void zip (File srcDir, File originSrcDir, ZipOutputStream dstStream) throws IOException {
    byte [] buffer = new byte [ZIP_BUFFER_SIZE];
    int bytes = 0;
    String [] dirList = srcDir.list ();
    for (int i = 0;
    i < dirList.length; i ++) {
        File file = new File (srcDir, dirList [i]);
        if (file.isDirectory ()) {
            zip (file, originSrcDir, dstStream);
            continue;
        }
        FileInputStream fis = new FileInputStream (file);
        ZipEntry entry = new ZipEntry (TFileHandler.removeDirectoryPath (originSrcDir.getAbsolutePath (), file.getAbsolutePath ()));
        dstStream.putNextEntry (entry);
        while ((bytes = fis.read (buffer)) != - 1) dstStream.write (buffer, 0, bytes);

        fis.close ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
1282532,"void initOut () throws IOException {
    if (zipped) {
        zout = new ZipOutputStream (sink);
        zout.putNextEntry (new ZipEntry (""file.xml""));
        this.xout = new OutputStreamWriter (zout, ""UTF8"");
    } else {
        this.xout = new OutputStreamWriter (sink, ""UTF8"");
    }
}
",13877913,"public static boolean addZipEntry (String srcZipFile, String newEntryFile, String dstFile) {
    java.util.zip.ZipOutputStream zout = null;
    InputStream is = null;
    try {
        if (new File (newEntryFile).isDirectory () && ! newEntryFile.substring (newEntryFile.length () - 1).equals (File.separator)) {
            newEntryFile = newEntryFile + File.separator;
        }
        System.err.println (""============"");
        File fn = new File (dstFile);
        if (! fn.exists ()) {
            fn.createNewFile ();
        }
        zout = new java.util.zip.ZipOutputStream (new FileOutputStream (dstFile));
        ZipFile zipfile = new ZipFile (srcZipFile);
        ZipEntry entry = null;
        Enumeration e = zipfile.entries ();
        byte [] buffer = new byte [1024];
        while (e.hasMoreElements ()) {
            entry = (ZipEntry) e.nextElement ();
            System.err.println (entry.getName ());
            zout.putNextEntry (entry);
            is = new BufferedInputStream (zipfile.getInputStream (entry));
            int count;
            while ((count = is.read (buffer, 0, 1024)) != - 1) {
                zout.write (buffer, 0, count);
                zout.flush ();
            }
            is.close ();
            zout.closeEntry ();
        }
        zipFile (null, newEntryFile, ""*.*"", zout);
        zout.close ();
        return true;
    } catch (java.io.IOException ioex) {
        LogUtil.getLogger ().error (ioex.getMessage (), ioex);
        ioex.printStackTrace ();
        return false;
    } finally {
        try {
            if (zout != null) {
                zout.close ();
            }
        } catch (Exception ex) {
        }
        try {
            if (is != null) {
                is.close ();
            }
        } catch (Exception ex) {
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
4932279,"public void testSavepoint4 () throws Exception {
    Statement stmt = con.createStatement ();
    stmt.execute (""CREATE TABLE #savepoint4 (data int)"");
    stmt.close ();
    con.setAutoCommit (false);
    for (int i = 0;
    i < 3; i ++) {
        PreparedStatement pstmt = con.prepareStatement (""INSERT INTO #savepoint4 (data) VALUES (?)"");
        pstmt.setInt (1, 1);
        assertTrue (pstmt.executeUpdate () == 1);
        Savepoint savepoint = con.setSavepoint ();
        assertNotNull (savepoint);
        assertTrue (savepoint.getSavepointId () == 1);
        try {
            savepoint.getSavepointName ();
            assertTrue (false);
        } catch (SQLException e) {
        }
        pstmt.setInt (1, 2);
        assertTrue (pstmt.executeUpdate () == 1);
        pstmt.close ();
        pstmt = con.prepareStatement (""SELECT SUM(data) FROM #savepoint4"");
        ResultSet rs = pstmt.executeQuery ();
        assertTrue (rs.next ());
        assertTrue (rs.getInt (1) == 3);
        assertTrue (! rs.next ());
        pstmt.close ();
        rs.close ();
        con.rollback (savepoint);
        pstmt = con.prepareStatement (""SELECT SUM(data) FROM #savepoint4"");
        rs = pstmt.executeQuery ();
        assertTrue (rs.next ());
        assertTrue (rs.getInt (1) == 1);
        assertTrue (! rs.next ());
        pstmt.close ();
        rs.close ();
        con.rollback ();
    }
    con.setAutoCommit (true);
}
",19147301,"public boolean actualizarIdPartida (int idJugadorDiv, int idRonda, int idPartida) {
    int intResult = 0;
    String sql = ""UPDATE jugadorxdivxronda "" + "" SET idPartida = "" + idPartida + "" WHERE jugadorxDivision_idJugadorxDivision = "" + idJugadorDiv + "" AND ronda_numeroRonda = "" + idRonda;
    try {
        connection = conexionBD.getConnection ();
        connection.setAutoCommit (false);
        ps = connection.prepareStatement (sql);
        intResult = ps.executeUpdate ();
        connection.commit ();
    } catch (SQLException ex) {
        ex.printStackTrace ();
        try {
            connection.rollback ();
        } catch (SQLException exe) {
            exe.printStackTrace ();
        }
    } finally {
        conexionBD.close (ps);
        conexionBD.close (connection);
    }
    return (intResult > 0);
}
",Execute update and rollback.,Type-3 (WT3/4),TRUE
1023289,"public static String MD5 (String s) {
    try {
        MessageDigest m = MessageDigest.getInstance (""MD5"");
        m.update (s.getBytes (), 0, s.length ());
        return new BigInteger (1, m.digest ()).toString (16);
    } catch (NoSuchAlgorithmException ex) {
        return """";
    }
}
",14032835,"private byte [] szyfrujKlucz (byte [] kluczSesyjny) {
    byte [] zaszyfrowanyKlucz = null;
    byte [] klucz = null;
    try {
        MessageDigest skrot = MessageDigest.getInstance (""SHA-1"");
        skrot.update (haslo.getBytes ());
        byte [] skrotHasla = skrot.digest ();
        Object kluczDoKlucza = MARS_Algorithm.makeKey (skrotHasla);
        int resztaKlucza = this.dlugoscKlucza % ROZMIAR_BLOKU;
        if (resztaKlucza == 0) {
            klucz = kluczSesyjny;
            zaszyfrowanyKlucz = new byte [this.dlugoscKlucza];
        } else {
            int liczbaBlokow = this.dlugoscKlucza / ROZMIAR_BLOKU + 1;
            int nowyRozmiar = liczbaBlokow * ROZMIAR_BLOKU;
            zaszyfrowanyKlucz = new byte [nowyRozmiar];
            klucz = new byte [nowyRozmiar];
            byte roznica = (byte) (ROZMIAR_BLOKU - resztaKlucza);
            System.arraycopy (kluczSesyjny, 0, klucz, 0, kluczSesyjny.length);
            for (int i = kluczSesyjny.length;
            i < nowyRozmiar; i ++) klucz [i] = (byte) roznica;

        }
        byte [] szyfrogram = null;
        int liczbaBlokow = klucz.length / ROZMIAR_BLOKU;
        int offset = 0;
        for (offset = 0; offset < liczbaBlokow; offset ++) {
            szyfrogram = MARS_Algorithm.blockEncrypt (klucz, offset * ROZMIAR_BLOKU, kluczDoKlucza);
            System.arraycopy (szyfrogram, 0, zaszyfrowanyKlucz, offset * ROZMIAR_BLOKU, szyfrogram.length);
        }
    } catch (InvalidKeyException ex) {
        Logger.getLogger (SzyfrowaniePliku.class.getName ()).log (Level.SEVERE, null, ex);
    } catch (NoSuchAlgorithmException ex) {
        ex.printStackTrace ();
    }
    return zaszyfrowanyKlucz;
}
",Secure Hash,Type-3 (WT3/4),TRUE
1287483,"protected void doGet (HttpServletRequest req, HttpServletResponse response) throws ServletException, IOException {
    keysString = req.getParameter (""resultKeys"");
    if (req.getParameter (""mode"") != null && ! req.getParameter (""mode"").equals ("""")) {
        archiveHelper.setMode (req.getParameter (""mode""));
    }
    SecurityAdvisor secAdvisor = null;
    try {
        secAdvisor = (SecurityAdvisor) req.getSession ().getAttribute (SecurityAdvisor.SECURITY_ADVISOR_SESSION_KEY);
        if (secAdvisor != null) {
            response.setContentType (""application/x-download"");
            response.setHeader (""Content-Disposition"", ""attachment;filename=microarray.zip"");
            response.setHeader (""Cache-Control"", ""max-age=0, must-revalidate"");
            long time1 = System.currentTimeMillis ();
            Session sess = secAdvisor.getHibernateSession (req.getUserPrincipal () != null ? req.getUserPrincipal ().getName () : ""guest"");
            DictionaryHelper dh = DictionaryHelper.getInstance (sess);
            baseDir = dh.getAnalysisReadDirectory (req.getServerName ());
            archiveHelper.setTempDir (dh.getPropertyDictionary (PropertyDictionary.TEMP_DIRECTORY));
            Map fileNameMap = new HashMap ();
            long compressedFileSizeTotal = getFileNamesToDownload (baseDir, keysString, fileNameMap);
            ZipOutputStream zipOut = null;
            TarArchiveOutputStream tarOut = null;
            if (archiveHelper.isZipMode ()) {
                zipOut = new ZipOutputStream (response.getOutputStream ());
            } else {
                tarOut = new TarArchiveOutputStream (response.getOutputStream ());
            }
            int totalArchiveSize = 0;
            for (Iterator i = fileNameMap.keySet ().iterator ();
            i.hasNext ();) {
                String analysisNumber = (String) i.next ();
                Analysis analysis = null;
                List analysisList = sess.createQuery (""SELECT a from Analysis a where a.number = '"" + analysisNumber + ""'"").list ();
                if (analysisList.size () == 1) {
                    analysis = (Analysis) analysisList.get (0);
                }
                if (analysis == null) {
                    log.error (""Unable to find request "" + analysisNumber + "".  Bypassing download for user "" + req.getUserPrincipal ().getName () + ""."");
                    continue;
                }
                if (! secAdvisor.canRead (analysis)) {
                    log.error (""Insufficient permissions to read analysis "" + analysisNumber + "".  Bypassing download for user "" + req.getUserPrincipal ().getName () + ""."");
                    continue;
                }
                List fileNames = (List) fileNameMap.get (analysisNumber);
                for (Iterator i1 = fileNames.iterator ();
                i1.hasNext ();) {
                    String filename = (String) i1.next ();
                    String zipEntryName = ""bioinformatics-analysis-"" + filename.substring (baseDir.length ());
                    archiveHelper.setArchiveEntryName (zipEntryName);
                    TransferLog xferLog = new TransferLog ();
                    xferLog.setFileName (filename.substring (baseDir.length () + 5));
                    xferLog.setStartDateTime (new java.util.Date (System.currentTimeMillis ()));
                    xferLog.setTransferType (TransferLog.TYPE_DOWNLOAD);
                    xferLog.setTransferMethod (TransferLog.METHOD_HTTP);
                    xferLog.setPerformCompression (""Y"");
                    xferLog.setIdAnalysis (analysis.getIdAnalysis ());
                    xferLog.setIdLab (analysis.getIdLab ());
                    InputStream in = archiveHelper.getInputStreamToArchive (filename, zipEntryName);
                    ZipEntry zipEntry = null;
                    if (archiveHelper.isZipMode ()) {
                        zipEntry = new ZipEntry (archiveHelper.getArchiveEntryName ());
                        zipOut.putNextEntry (zipEntry);
                    } else {
                        TarArchiveEntry entry = new TarArchiveEntry (archiveHelper.getArchiveEntryName ());
                        entry.setSize (archiveHelper.getArchiveFileSize ());
                        tarOut.putArchiveEntry (entry);
                    }
                    OutputStream out = null;
                    if (archiveHelper.isZipMode ()) {
                        out = zipOut;
                    } else {
                        out = tarOut;
                    }
                    int size = archiveHelper.transferBytes (in, out);
                    totalArchiveSize += size;
                    xferLog.setFileSize (new BigDecimal (size));
                    xferLog.setEndDateTime (new java.util.Date (System.currentTimeMillis ()));
                    sess.save (xferLog);
                    if (archiveHelper.isZipMode ()) {
                        zipOut.closeEntry ();
                        totalArchiveSize += zipEntry.getCompressedSize ();
                    } else {
                        tarOut.closeArchiveEntry ();
                        totalArchiveSize += archiveHelper.getArchiveFileSize ();
                    }
                    archiveHelper.removeTemporaryFile ();
                }
                sess.flush ();
            }
            response.setContentLength (totalArchiveSize);
            if (archiveHelper.isZipMode ()) {
                zipOut.finish ();
                zipOut.flush ();
            } else {
                tarOut.close ();
                tarOut.flush ();
            }
        } else {
            response.setStatus (999);
            System.out.println (""DownloadAnalyisFolderServlet: You must have a SecurityAdvisor in order to run this command."");
        }
    } catch (Exception e) {
        response.setStatus (999);
        System.out.println (""DownloadAnalyisFolderServlet: An exception occurred "" + e.toString ());
        e.printStackTrace ();
    } finally {
        if (secAdvisor != null) {
            try {
                secAdvisor.closeHibernateSession ();
            } catch (Exception e) {
            }
        }
        archiveHelper.removeTemporaryFile ();
    }
}
",18643979,"private static void addTargetFile (ZipOutputStream zos, File file) throws FileNotFoundException, ZipException, IOException {
    try {
        BufferedInputStream bis = new BufferedInputStream (new FileInputStream (file));
        String file_path = file.getPath ();
        if (file_path.startsWith (OctopusApplication.PATH_EXPORT_FOLDER)) {
            file_path = file_path.substring (OctopusApplication.PATH_EXPORT_FOLDER.length (), file_path.length ());
        }
        ZipEntry target = new ZipEntry (file_path);
        zos.putNextEntry (target);
        int c;
        while ((c = bis.read ()) != - 1) {
            zos.write ((byte) c);
        }
        bis.close ();
        zos.closeEntry ();
    } catch (FileNotFoundException e) {
        throw e;
    } catch (ZipException e) {
        throw e;
    } catch (IOException e) {
        throw e;
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
4140310,"public boolean verify (final char [] password, final String encryptedPassword) {
    MessageDigest digest = null;
    int size = 0;
    String base64 = null;
    if (encryptedPassword.regionMatches (true, 0, ""{SHA}"", 0, 5)) {
        size = 20;
        base64 = encryptedPassword.substring (5);
        try {
            digest = MessageDigest.getInstance (""SHA-1"");
        } catch (final NoSuchAlgorithmException e) {
            throw new IllegalStateException (""Invalid algorithm"");
        }
    } else if (encryptedPassword.regionMatches (true, 0, ""{SSHA}"", 0, 6)) {
        size = 20;
        base64 = encryptedPassword.substring (6);
        try {
            digest = MessageDigest.getInstance (""SHA-1"");
        } catch (final NoSuchAlgorithmException e) {
            throw new IllegalStateException (""Invalid algorithm"");
        }
    } else if (encryptedPassword.regionMatches (true, 0, ""{MD5}"", 0, 5)) {
        size = 16;
        base64 = encryptedPassword.substring (5);
        try {
            digest = MessageDigest.getInstance (""MD5"");
        } catch (final NoSuchAlgorithmException e) {
            throw new IllegalStateException (""Invalid algorithm"");
        }
    } else if (encryptedPassword.regionMatches (true, 0, ""{SMD5}"", 0, 6)) {
        size = 16;
        base64 = encryptedPassword.substring (6);
        try {
            digest = MessageDigest.getInstance (""MD5"");
        } catch (final NoSuchAlgorithmException e) {
            throw new IllegalStateException (""Invalid algorithm"");
        }
    } else {
        return false;
    }

    try {
        final byte [] data = Base64.decodeBase64 (base64.getBytes (""UTF-8""));
        final byte [] orig = new byte [size];
        System.arraycopy (data, 0, orig, 0, size);
        digest.reset ();
        digest.update (new String (password).getBytes (""UTF-8""));
        if (data.length > size) {
            digest.update (data, size, data.length - size);
        }
        return MessageDigest.isEqual (digest.digest (), orig);
    } catch (UnsupportedEncodingException e) {
        throw new IllegalStateException (""UTF-8 Unsupported"");
    }
}
",6659731,"public static String hashStringMD5 (String string) throws NoSuchAlgorithmException {
    MessageDigest md = MessageDigest.getInstance (""MD5"");
    md.update (string.getBytes ());
    byte byteData [] = md.digest ();
    StringBuffer sb = new StringBuffer ();
    for (int i = 0;
    i < byteData.length; i ++) {
        sb.append (Integer.toString ((byteData [i] & 0xff) + 0x100, 16).substring (1));
    }
    StringBuffer hexString = new StringBuffer ();
    for (int i = 0;
    i < byteData.length; i ++) {
        String hex = Integer.toHexString (0xff & byteData [i]);
        if (hex.length () == 1) hexString.append ('0');

        hexString.append (hex);
    }
    return hexString.toString ();
}
",Secure Hash,Type-3 (WT3/4),TRUE
945981,"private void displayDiffResults () throws IOException {
    File outFile = File.createTempFile (""diff"", "".htm"");
    outFile.deleteOnExit ();
    FileOutputStream outStream = new FileOutputStream (outFile);
    BufferedWriter out = new BufferedWriter (new OutputStreamWriter (outStream));
    out.write (""<html><head><title>LOC Differences</title>\n"" + SCRIPT + ""</head>\n"" + ""<body bgcolor='#ffffff'>\n"" + ""<div onMouseOver=\""window.defaultStatus='Metrics'\"">\n"");
    if (addedTable.length () > 0) {
        out.write (""<table border><tr><th>Files Added:</th>"" + ""<th>Add</th><th>Type</th></tr>"");
        out.write (addedTable.toString ());
        out.write (""</table><br><br>"");
    }
    if (modifiedTable.length () > 0) {
        out.write (""<table border><tr><th>Files Modified:</th>"" + ""<th>Base</th><th>Del</th><th>Mod</th><th>Add</th>"" + ""<th>Total</th><th>Type</th></tr>"");
        out.write (modifiedTable.toString ());
        out.write (""</table><br><br>"");
    }
    if (deletedTable.length () > 0) {
        out.write (""<table border><tr><th>Files Deleted:</th>"" + ""<th>Del</th><th>Type</th></tr>"");
        out.write (deletedTable.toString ());
        out.write (""</table><br><br>"");
    }
    out.write (""<table name=METRICS BORDER>\n"");
    if (modifiedTable.length () > 0 || deletedTable.length () > 0) {
        out.write (""<tr><td>Base:&nbsp;</td><td>"");
        out.write (Long.toString (base));
        out.write (""</td></tr>\n<tr><td>Deleted:&nbsp;</td><td>"");
        out.write (Long.toString (deleted));
        out.write (""</td></tr>\n<tr><td>Modified:&nbsp;</td><td>"");
        out.write (Long.toString (modified));
        out.write (""</td></tr>\n<tr><td>Added:&nbsp;</td><td>"");
        out.write (Long.toString (added));
        out.write (""</td></tr>\n<tr><td>New & Changed:&nbsp;</td><td>"");
        out.write (Long.toString (added + modified));
        out.write (""</td></tr>\n"");
    }
    out.write (""<tr><td>Total:&nbsp;</td><td>"");
    out.write (Long.toString (total));
    out.write (""</td></tr>\n</table></div>"");
    redlinesOut.close ();
    out.flush ();
    InputStream redlines = new FileInputStream (redlinesTempFile);
    byte [] buffer = new byte [4096];
    int bytesRead;
    while ((bytesRead = redlines.read (buffer)) != - 1) outStream.write (buffer, 0, bytesRead);

    outStream.write (""</BODY></HTML>"".getBytes ());
    outStream.close ();
    Browser.launch (outFile.toURL ().toString ());
}
",12523607,"public void render (ServiceContext serviceContext) throws Exception {
    if (serviceContext.getTemplateName () == null) throw new Exception (""no Template defined for service: "" + serviceContext.getServiceInfo ().getRefName ());

    File f = new File (serviceContext.getTemplateName ());
    serviceContext.getResponse ().setContentLength ((int) f.length ());
    InputStream in = new FileInputStream (f);
    IOUtils.copy (in, serviceContext.getResponse ().getOutputStream (), 0, (int) f.length ());
    in.close ();
}
",Copy File,Type-3 (WT3/4),TRUE
1951108,"private void zipStream (InputStream inStream, String streamName, File zipFile) throws IOException {
    if (inStream == null) {
        log.warn (""No stream to zip."");
    } else {
        try {
            FileOutputStream dest = new FileOutputStream (zipFile);
            ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest));
            ZipEntry entry = new ZipEntry (streamName);
            out.putNextEntry (entry);
            copyInputStream (inStream, out);
            out.close ();
            dest.close ();
            inStream.close ();
        } catch (IOException e) {
            log.error (""IOException while zipping stream"");
            throw e;
        }
    }
}
",14787145,"public void setVariables (Properties varDef) throws Exception {
    sendMsg (""Setting  the variables ..."");
    outJar.putNextEntry (new ZipEntry (""vars""));
    ObjectOutputStream objOut = new ObjectOutputStream (outJar);
    objOut.writeObject (varDef);
    objOut.flush ();
    outJar.closeEntry ();
}
",Zip Files,Type-3 (WT3/4),FALSE
1121468,"private static PrintWriter getOut (int first, int last, String dir, String lang) throws IOException {
    if (dir == null) return null;

    File file = new File (dir, lang + "".wikipedia.zip"");
    if (! file.exists ()) file.createNewFile ();

    if (! file.canWrite ()) throw new IllegalArgumentException (""can't write "" + file);

    log (true, ""Writing Wikipedia events into "" + file.getAbsolutePath ());
    System.setProperty (""line.separator"", ""\n"");
    ZipOutputStream out = new ZipOutputStream (new FileOutputStream (file));
    out.putNextEntry (new ZipEntry (lang + "".wikipedia""));
    return new PrintWriter (new OutputStreamWriter (out, UTF8));
}
",23160103,"public void writeJar (JarOutputStream out) throws IOException, Pack200Exception {
    String [] fileName = fileBands.getFileName ();
    int [] fileModtime = fileBands.getFileModtime ();
    long [] fileSize = fileBands.getFileSize ();
    byte [] [] fileBits = fileBands.getFileBits ();
    int classNum = 0;
    int numberOfFiles = header.getNumberOfFiles ();
    long archiveModtime = header.getArchiveModtime ();
    for (int i = 0;
    i < numberOfFiles; i ++) {
        String name = fileName [i];
        long modtime = 1000 * (archiveModtime + fileModtime [i]);
        boolean deflate = fileDeflate [i];
        JarEntry entry = new JarEntry (name);
        if (deflate) {
            entry.setMethod (ZipEntry.DEFLATED);
        } else {
            entry.setMethod (ZipEntry.STORED);
            CRC32 crc = new CRC32 ();
            if (fileIsClass [i]) {
                crc.update (classFilesContents [classNum]);
                entry.setSize (classFilesContents [classNum].length);
            } else {
                crc.update (fileBits [i]);
                entry.setSize (fileSize [i]);
            }
            entry.setCrc (crc.getValue ());
        }
        entry.setTime (modtime - TimeZone.getDefault ().getRawOffset ());
        out.putNextEntry (entry);
        if (fileIsClass [i]) {
            entry.setSize (classFilesContents [classNum].length);
            out.write (classFilesContents [classNum]);
            classNum ++;
        } else {
            entry.setSize (fileSize [i]);
            out.write (fileBits [i]);
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
850680,"private static void readAndRewrite (File inFile, File outFile) throws IOException {
    ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile)));
    DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis);
    Dataset ds = DcmObjectFactory.getInstance ().newDataset ();
    dcmParser.setDcmHandler (ds.getDcmHandler ());
    dcmParser.parseDcmFile (null, Tags.PixelData);
    PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    System.out.println (""reading "" + inFile + ""..."");
    pdReader.readPixelData (false);
    ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile)));
    DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE;
    ds.writeDataset (out, dcmEncParam);
    ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ());
    System.out.println (""writing "" + outFile + ""..."");
    PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    pdWriter.writePixelData ();
    out.flush ();
    out.close ();
    System.out.println (""done!"");
}
",3024971,"@Test
public void testCopy_inputStreamToOutputStream_nullIn () throws Exception {
    OutputStream out = new ByteArrayOutputStream ();
    try {
        IOUtils.copy ((InputStream) null, out);
        fail ();
    } catch (NullPointerException ex) {
    }
}
",Copy File,Type-3 (WT3/4),TRUE
337322,"static void copy (String src, String dest) throws IOException {
    File ifp = new File (src);
    File ofp = new File (dest);
    if (ifp.exists () == false) {
        throw new IOException (""file '"" + src + ""' does not exist"");
    }
    FileInputStream fis = new FileInputStream (ifp);
    FileOutputStream fos = new FileOutputStream (ofp);
    byte [] b = new byte [1024];
    while (fis.read (b) > 0) fos.write (b);

    fis.close ();
    fos.close ();
}
",12859344,"private void sendFile (File file, HttpServletResponse response) throws IOException {
    response.setContentLength ((int) file.length ());
    InputStream inputStream = null;
    try {
        inputStream = new FileInputStream (file);
        IOUtils.copy (inputStream, response.getOutputStream ());
    } finally {
        IOUtils.closeQuietly (inputStream);
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1282532,"void initOut () throws IOException {
    if (zipped) {
        zout = new ZipOutputStream (sink);
        zout.putNextEntry (new ZipEntry (""file.xml""));
        this.xout = new OutputStreamWriter (zout, ""UTF8"");
    } else {
        this.xout = new OutputStreamWriter (sink, ""UTF8"");
    }
}
",16062997,"public static boolean zipDirectoryRecursive (File path, File zipFileName, String excludeRegEx, boolean relative, boolean compress) {
    ArrayList < File > filesToZip = new ArrayList < File > ();
    if (path.exists ()) {
        File [] files = path.listFiles ();
        for (int i = 0;
        i < files.length; i ++) {
            if (files [i].isDirectory ()) {
                FileTools.listFilesRecursive (files [i], filesToZip);
            } else {
                filesToZip.add (files [i]);
            }
        }
    }
    try {
        byte [] buffer = new byte [18024];
        ZipOutputStream out = new ZipOutputStream (new FileOutputStream (zipFileName));
        if (! compress) {
            out.setLevel (Deflater.NO_COMPRESSION);
        } else {
            out.setLevel (Deflater.DEFAULT_COMPRESSION);
        }
        for (int i = 0;
        i < filesToZip.size (); i ++) {
            if (excludeRegEx == null || ! filesToZip.get (i).getName ().contains (excludeRegEx)) {
                FileInputStream in = new FileInputStream (filesToZip.get (i));
                String filePath = filesToZip.get (i).getPath ();
                if (relative) {
                    filePath = filePath.replaceFirst (path.getAbsolutePath () + File.separator, """");
                }
                System.out.println (""Deflating: "" + filePath);
                out.putNextEntry (new ZipEntry (filePath));
                int len;
                while ((len = in.read (buffer)) > 0) {
                    out.write (buffer, 0, len);
                }
                out.closeEntry ();
                in.close ();
            }
        }
        out.close ();
    } catch (IllegalArgumentException iae) {
        iae.printStackTrace ();
        return (false);
    } catch (FileNotFoundException fnfe) {
        fnfe.printStackTrace ();
        return (false);
    } catch (IOException ioe) {
        ioe.printStackTrace ();
        return (false);
    }
    return (true);
}
",Zip Files,Type-3 (WT3/4),FALSE
6961676,"public void actionPerformed (ActionEvent e) {
    if (SAVEPICTURE.equals (e.getActionCommand ())) {
        byte [] data = ((PicturePane) picturesPane.getSelectedComponent ()).getImage ();
        if (data == null) {
            return;
        }
        File f = Util.getFile (this, ""Save file"", true);
        if (f != null) {
            try {
                Files.writeFile (f, data);
            } catch (Exception ex) {
                ex.printStackTrace ();
            }
        }
    } else if (SAVEDL.equals (e.getActionCommand ())) {
        JFileChooser fileChooser = new JFileChooser ();
        fileChooser.setFileFilter (net.sourceforge.scuba.util.Files.ZIP_FILE_FILTER);
        int choice = fileChooser.showSaveDialog (getContentPane ());
        switch (choice) {
            case JFileChooser.APPROVE_OPTION :
                try {
                    File file = fileChooser.getSelectedFile ();
                    FileOutputStream fileOut = new FileOutputStream (file);
                    ZipOutputStream zipOut = new ZipOutputStream (fileOut);
                    for (short fid : dl.getFileList ()) {
                        String entryName = Hex.shortToHexString (fid) + "".bin"";
                        InputStream dg = dl.getInputStream (fid);
                        zipOut.putNextEntry (new ZipEntry (entryName));
                        int bytesRead;
                        byte [] dgBytes = new byte [1024];
                        while ((bytesRead = dg.read (dgBytes)) > 0) {
                            zipOut.write (dgBytes, 0, bytesRead);
                        }
                        zipOut.closeEntry ();
                    }
                    zipOut.finish ();
                    zipOut.close ();
                    fileOut.flush ();
                    fileOut.close ();
                    break;
                } catch (IOException fnfe) {
                    fnfe.printStackTrace ();
                }
            default :
                break;
        }
    } else if (VIEWDOCCERT.equals (e.getActionCommand ())) {
        try {
            X509Certificate c = sodFile.getDocSigningCertificate ();
            viewData (c.toString (), c.getEncoded ());
        } catch (Exception ex) {
            ex.printStackTrace ();
        }
    } else if (VIEWAAKEY.equals (e.getActionCommand ())) {
        PublicKey k = dg13file.getPublicKey ();
        viewData (k.toString (), k.getEncoded ());
    } else if (VIEWEAPKEYS.equals (e.getActionCommand ())) {
        String s = """";
        int count = 0;
        Set < Integer > ids = dg14file.getIds ();
        List < byte [] > keys = new ArrayList < byte [] > ();
        for (Integer id : ids) {
            if (count != 0) {
                s += ""\n"";
            }
            if (id != - 1) {
                s += ""Key identifier: "" + id + ""\n"";
            }
            PublicKey k = dg14file.getKey (id);
            s += k.toString ();
            keys.add (k.getEncoded ());
            count ++;
        }
        viewData (s, keys);
    }

}
",8954798,"public static void writeProject (ProjectModel projectModel, String path) throws IOException {
    log.info (""Writing project file to "" + path);
    File file = JDemResourceLoader.getAsFile (path);
    ZipOutputStream zos = new ZipOutputStream (new BufferedOutputStream (new FileOutputStream (file)));
    ZipEntry settingsEntry = new ZipEntry (""project.json"");
    zos.putNextEntry (settingsEntry);
    JsonProjectFileWriter.writeProject (projectModel, zos);
    if (projectModel.getUserScript () != null) {
        ZipEntry scriptEntry = null;
        if (projectModel.getScriptLanguage () == ScriptLanguageEnum.GROOVY) {
            scriptEntry = new ZipEntry (""script.groovy"");
        } else if (projectModel.getScriptLanguage () == ScriptLanguageEnum.JYTHON) {
            scriptEntry = new ZipEntry (""script.py"");
        }

        if (scriptEntry != null) {
            zos.putNextEntry (scriptEntry);
            zos.write (projectModel.getUserScript ().getBytes ());
        }
    } else {
        log.info (""User script is null, cannot write."");
    }
    zos.close ();
}
",Zip Files,Type-3 (WT3/4),TRUE
5389884,"public static long getDummyCRC (long count) throws IOException {
    CRC32 crc = new CRC32 ();
    byte [] data = new byte [1024];
    int done = 0;
    while (done < count) {
        int tbw = (int) Math.min (count - done, data.length);
        crc.update (data, 0, tbw);
        done += tbw;
    }
    return crc.getValue ();
}
",8849605,"public void decode (File input) throws DecoderException {
    try {
        YEncFile yencFile = new YEncFile (input);
        StringBuffer outputName = new StringBuffer (outputDirName);
        outputName.append (File.separator);
        outputName.append (yencFile.getHeader ().getName ());
        RandomAccessFile output = new RandomAccessFile (outputName.toString (), ""rw"");
        long pos = yencFile.getDataBegin ();
        yencFile.getInput ().seek (pos);
        ByteArrayOutputStream baos = new ByteArrayOutputStream ();
        while (pos < yencFile.getDataEnd ()) {
            baos.write (yencFile.getInput ().read ());
            pos ++;
        }
        byte [] buff = decoder.decode (baos.toByteArray ());
        output.write (buff);
        output.close ();
        CRC32 crc32 = new CRC32 ();
        crc32.update (buff);
        if (! yencFile.getTrailer ().getCrc32 ().equals (Long.toHexString (crc32.getValue ()).toUpperCase ())) throw new DecoderException (""Error in CRC32 check."");

    } catch (YEncException ye) {
        throw new DecoderException (""Input file is not a YEnc file or contains error : "" + ye.getMessage ());
    } catch (FileNotFoundException fnfe) {
        throw new DecoderException (""Enable to create output file : "" + fnfe.getMessage ());
    } catch (IOException ioe) {
        throw new DecoderException (""Enable to read input file : "" + ioe.getMessage ());
    }
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
6168797,"public byte [] buildPacket (int padding, SecureRandom random) {
    byte [] packet = new byte [PACKET_SIZE + padding];
    byte [] buffer = m_buffer.getBytes ();
    if (random != null) {
        random.nextBytes (packet);
    } else {
        for (int i = 10 + buffer.length;
        i < packet.length; i ++) {
            packet [i] = 0;
        }
    }
    packet [0] = (byte) ((m_version>> 8) & 0xff);
    packet [1] = (byte) (m_version & 0xff);
    packet [2] = (byte) ((m_type>> 8) & 0xff);
    packet [3] = (byte) (m_type & 0xff);
    packet [4] = 0;
    packet [5] = 0;
    packet [6] = 0;
    packet [7] = 0;
    packet [8] = (byte) ((m_resultCode>> 8) & 0xff);
    packet [9] = (byte) (m_resultCode & 0xff);
    System.arraycopy (buffer, 0, packet, 10, buffer.length);
    if ((10 + buffer.length) < PACKET_SIZE - 1) {
        packet [10 + buffer.length] = 0;
    }
    packet [PACKET_SIZE - 1] = 0;
    CRC32 crc = new CRC32 ();
    crc.update (packet);
    long crc_l = crc.getValue ();
    packet [4] = (byte) ((crc_l>> 24) & 0xff);
    packet [5] = (byte) ((crc_l>> 16) & 0xff);
    packet [6] = (byte) ((crc_l>> 8) & 0xff);
    packet [7] = (byte) (crc_l & 0xff);
    return packet;
}
",8653093,"public static boolean decode (String fileName, ByteArrayOutputStream bos) throws IOException {
    byte [] buffer = new byte [BUFFERSIZE];
    int bufferLength = 0;
    BufferedReader file = new BufferedReader (new InputStreamReader (new FileInputStream (fileName)));
    String line = file.readLine ();
    while (line != null && ! line.startsWith (""=ybegin"")) {
        line = file.readLine ();
    }
    if (line == null) throw new IOException (""Error while looking for start of a file.  Could not locate line starting with \""=ybegin\""."");

    fileName = parseForName (line);
    if (fileName == null) fileName = ""Unknown.blob"";

    String partNo = parseForString (line, ""part"");
    if (partNo != null) {
        while (line != null && ! line.startsWith (""=ypart"")) {
            line = file.readLine ();
        }
        if (line == null) throw new IOException (""Error while handling a multipart file.  Could not locate line starting with \""=ypart\""."");

    }
    int character;
    boolean special = false;
    line = file.readLine ();
    CRC32 crc = new CRC32 ();
    while (line != null && ! line.startsWith (""=yend"")) {
        for (int lcv = 0;
        lcv < line.length (); lcv ++) {
            character = (int) line.charAt (lcv);
            if (character != 61) {
                buffer [bufferLength] = (byte) (special ? character - 106 : character - 42);
                bufferLength ++;
                if (bufferLength == BUFFERSIZE) {
                    bos.write (buffer);
                    crc.update (buffer);
                    bufferLength = 0;
                }
                special = false;
            } else special = true;

        }
        line = file.readLine ();
    }
    if (bufferLength > 0) {
        bos.write (buffer, 0, bufferLength);
        crc.update (buffer, 0, bufferLength);
    }
    file.close ();
    Debug.debug (""Size of output file = "" + bos.size ());
    if (line != null && line.startsWith (""=yend"")) {
        long fileCRC = - 1;
        String crcVal = parseForString (line, ""pcrc32"");
        if (crcVal == null) {
            crcVal = parseForCRC (line);
        }
        if (crcVal != null) fileCRC = Long.parseLong (crcVal, 16);

        return fileCRC == crc.getValue ();
    } else return false;

}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
5936119,"public boolean batchFinished () throws Exception {
    Instances data = getInputFormat ();
    if (data == null) throw new IllegalStateException (""No input instance format defined"");

    if (m_Converter == null) {
        int [] randomIndices = new int [m_ClassCounts.length];
        for (int i = 0;
        i < randomIndices.length; i ++) {
            randomIndices [i] = i;
        }
        for (int j = randomIndices.length - 1;
        j > 0; j --) {
            int toSwap = m_Random.nextInt (j + 1);
            int tmpIndex = randomIndices [j];
            randomIndices [j] = randomIndices [toSwap];
            randomIndices [toSwap] = tmpIndex;
        }
        double [] randomizedCounts = new double [m_ClassCounts.length];
        for (int i = 0;
        i < randomizedCounts.length; i ++) {
            randomizedCounts [i] = m_ClassCounts [randomIndices [i]];
        }
        if (m_ClassOrder == RANDOM) {
            m_Converter = randomIndices;
            m_ClassCounts = randomizedCounts;
        } else {
            int [] sorted = Utils.sort (randomizedCounts);
            m_Converter = new int [sorted.length];
            if (m_ClassOrder == FREQ_ASCEND) {
                for (int i = 0;
                i < sorted.length; i ++) {
                    m_Converter [i] = randomIndices [sorted [i]];
                }
            } else if (m_ClassOrder == FREQ_DESCEND) {
                for (int i = 0;
                i < sorted.length; i ++) {
                    m_Converter [i] = randomIndices [sorted [sorted.length - i - 1]];
                }
            } else {
                throw new IllegalArgumentException (""Class order not defined!"");
            }

            double [] tmp2 = new double [m_ClassCounts.length];
            for (int i = 0;
            i < m_Converter.length; i ++) {
                tmp2 [i] = m_ClassCounts [m_Converter [i]];
            }
            m_ClassCounts = tmp2;
        }
        FastVector values = new FastVector (data.classAttribute ().numValues ());
        for (int i = 0;
        i < data.numClasses (); i ++) {
            values.addElement (data.classAttribute ().value (m_Converter [i]));
        }
        FastVector newVec = new FastVector (data.numAttributes ());
        for (int i = 0;
        i < data.numAttributes (); i ++) {
            if (i == data.classIndex ()) {
                newVec.addElement (new Attribute (data.classAttribute ().name (), values, data.classAttribute ().getMetadata ()));
            } else {
                newVec.addElement (data.attribute (i));
            }
        }
        Instances newInsts = new Instances (data.relationName (), newVec, 0);
        newInsts.setClassIndex (data.classIndex ());
        setOutputFormat (newInsts);
        int [] temp = new int [m_Converter.length];
        for (int i = 0;
        i < temp.length; i ++) {
            temp [m_Converter [i]] = i;
        }
        m_Converter = temp;
        for (int xyz = 0;
        xyz < data.numInstances (); xyz ++) {
            Instance datum = data.instance (xyz);
            if (! datum.isMissing (datum.classIndex ())) {
                datum.setClassValue ((float) m_Converter [(int) datum.classValue ()]);
            }
            push (datum);
        }
    }
    flushInput ();
    m_NewBatch = true;
    return (numPendingOutput () != 0);
}
",16380022,"public void shuffle (Random rand) {
    for (int i = cards.length - 1;
    i >= 0; i --) {
        int r = rand.nextInt (i + 1);
        Card t = cards [i];
        cards [i] = cards [r];
        cards [r] = t;
    }
    nextCard = 0;
}
",Shuffle Array in Place,Type-3 (WT3/4),FALSE
150036,"public static long compute (String str) {
    CRC32 crc = new CRC32 ();
    Adler32 adler = new Adler32 ();
    crc.update (str.getBytes ());
    adler.update (str.getBytes ());
    long dg1 = crc.getValue ();
    long dg2 = adler.getValue ();
    crc.update (String.valueOf (dg2).getBytes ());
    adler.update (String.valueOf (dg1).getBytes ());
    long d3 = crc.getValue ();
    long d4 = adler.getValue ();
    dg1 ^= d4;
    dg2 ^= d3;
    return (dg2 ^ ((dg1>>> 32) | (dg1 << 32)));
}
",10905580,"public String getID () {
    CRC32 checksum = new CRC32 ();
    int i = 0;
    checksum.reset ();
    while ((i < data.length ()) && (i < 5000)) {
        checksum.update ((int) data.charAt (i));
        i ++;
    }
    return (Long.toHexString (checksum.getValue ()) + Integer.toHexString (data.hashCode ()));
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
1262021,"public void execute () throws BuildException {
    boolean manifestFound = false;
    ZipFile zipFile = null;
    ZipInputStream zipInputStream = null;
    ZipOutputStream zipFileOutputStream = null;
    FileInputStream fileInputStream = null;
    File fileIn = new File (m_jarPath);
    if (! fileIn.exists ()) {
        throw new BuildException (""File "" + m_jarPath + "" does not exists."");
    }
    File fileOut = new File (m_jarPath + "".new"");
    try {
        zipFile = new ZipFile (fileIn);
        fileInputStream = new FileInputStream (fileIn);
        zipInputStream = new ZipInputStream (fileInputStream);
        FileOutputStream fileOutputStream = new FileOutputStream (fileOut);
        zipFileOutputStream = new ZipOutputStream (fileOutputStream);
        ZipEntry entry = zipInputStream.getNextEntry ();
        while (entry != null) {
            if (entry.isDirectory ()) {
            } else {
                InputStream in = zipFile.getInputStream (entry);
                byte [] content = readInputStream (in);
                if (entry.getName ().endsWith (""manifest.mf"")) {
                    manifestFound = true;
                    String contenu = incrementVersionInManifest (content);
                    zipFileOutputStream.putNextEntry (entry);
                    zipFileOutputStream.write (contenu.getBytes ());
                    zipFileOutputStream.flush ();
                } else {
                    zipFileOutputStream.putNextEntry (entry);
                    zipFileOutputStream.write (content);
                    zipFileOutputStream.flush ();
                }
            }
            entry = zipInputStream.getNextEntry ();
        }
        if (! manifestFound) {
            ZipEntry newEntry = new ZipEntry (""/meta-inf/manifest.mf"");
            zipFileOutputStream.putNextEntry (newEntry);
            if (m_newMajorRelease == null) {
                m_newMajorRelease = ""1.0"";
            }
            if (m_newMinorRelease == null) {
                m_newMinorRelease = ""1"";
            }
            String content = ""Manifest-Version: "" + m_newMajorRelease + ""\nImplementation-Version: \""Build ("" + m_newMinorRelease + "")\"""";
            if ((m_envType != null) && (m_envType.length () > 0)) {
                content += (ENVTYPE_HEADER_STRING + m_envType + ""\n"");
            }
            zipFileOutputStream.write (content.getBytes ());
            zipFileOutputStream.flush ();
            m_newVersion = m_newMajorRelease + ""."" + m_newMinorRelease;
        }
    } catch (Exception e) {
        throw new BuildException (e.getMessage (), e);
    } finally {
        try {
            if (zipFileOutputStream != null) {
                zipFileOutputStream.close ();
            }
            if (zipInputStream != null) {
                zipInputStream.close ();
            }
            if (zipFile != null) {
                zipFile.close ();
            }
        } catch (IOException e) {
        }
    }
    fileIn.delete ();
    fileOut.renameTo (fileIn);
    System.out.println (""Version increased in jar "" + m_jarPath + "" to "" + m_newVersion);
}
",1669328,"public static byte [] zipEntriesAndFiles (Map < ZipEntry, byte [] > files) throws Exception {
    ByteArrayOutputStream dest = new ByteArrayOutputStream ();
    ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest));
    byte [] data = new byte [2048];
    Iterator < ZipEntry > itr = files.keySet ().iterator ();
    while (itr.hasNext ()) {
        ZipEntry entry = itr.next ();
        byte [] tempFile = files.get (entry);
        ByteArrayInputStream bytesIn = new ByteArrayInputStream (tempFile);
        BufferedInputStream origin = new BufferedInputStream (bytesIn, 2048);
        out.putNextEntry (entry);
        int count;
        while ((count = origin.read (data, 0, 2048)) != - 1) {
            out.write (data, 0, count);
        }
        bytesIn.close ();
        origin.close ();
    }
    out.close ();
    byte [] outBytes = dest.toByteArray ();
    dest.close ();
    return outBytes;
}
",Zip Files,Type-3 (WT3/4),FALSE
606859,"private static void readAndRewrite (File inFile, File outFile) throws IOException {
    ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile)));
    DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis);
    Dataset ds = DcmObjectFactory.getInstance ().newDataset ();
    dcmParser.setDcmHandler (ds.getDcmHandler ());
    dcmParser.parseDcmFile (null, Tags.PixelData);
    PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    System.out.println (""reading "" + inFile + ""..."");
    pdReader.readPixelData (false);
    ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile)));
    DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE;
    ds.writeDataset (out, dcmEncParam);
    ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ());
    System.out.println (""writing "" + outFile + ""..."");
    PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    pdWriter.writePixelData ();
    out.flush ();
    out.close ();
    System.out.println (""done!"");
}
",21834878,"protected void renderResource (final HttpServletRequest request, final HttpServletResponse response, final InputStream is) throws IOException {
    try {
        IOUtils.copy (is, response.getOutputStream ());
    } finally {
        IOUtils.closeQuietly (is);
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1446727,"private void backupDiskFile (ZipOutputStream out, String fileName, DiskFile file) throws SQLException, IOException {
    Database db = session.getDatabase ();
    fileName = FileUtils.getFileName (fileName);
    out.putNextEntry (new ZipEntry (fileName));
    int pos = - 1;
    int max = file.getReadCount ();
    while (true) {
        pos = file.copyDirect (pos, out);
        if (pos < 0) {
            break;
        }
        db.setProgress (DatabaseEventListener.STATE_BACKUP_FILE, fileName, pos, max);
    }
    out.closeEntry ();
}
",16900371,"private void addAllUploadedFiles (Environment en, ZipOutputStream zipout, int progressStart, int progressLength) throws IOException, FileNotFoundException {
    File uploadPath = en.uploadPath (virtualWiki, """");
    String [] files = uploadPath.list ();
    int bytesRead = 0;
    byte byteArray [] = new byte [4096];
    for (int i = 0;
    i < files.length; i ++) {
        String fileName = files [i];
        File file = en.uploadPath (virtualWiki, fileName);
        if (file.isDirectory ()) {
            continue;
        }
        progress = Math.min (progressStart + (int) ((double) i * (double) progressLength / files.length), 99);
        logger.fine (""Adding uploaded file "" + fileName);
        ZipEntry entry = new ZipEntry (safename (fileName));
        try {
            FileInputStream in = new FileInputStream (file);
            zipout.putNextEntry (entry);
            while (in.available () > 0) {
                bytesRead = in.read (byteArray, 0, Math.min (4096, in.available ()));
                zipout.write (byteArray, 0, bytesRead);
            }
            zipout.closeEntry ();
            zipout.flush ();
        } catch (FileNotFoundException e) {
            logger.log (Level.WARNING, ""Could not open file!"", e);
        } catch (IOException e) {
            logger.log (Level.WARNING, ""IOException!"", e);
            try {
                zipout.closeEntry ();
                zipout.flush ();
            } catch (IOException e1) {
            }
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
732800,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",6973739,"private void writeManifestEntry (File f, JarOutputStream out) {
    byte [] buffer = new byte [BUFFERSIZE];
    int bytes_read;
    try {
        BufferedInputStream in = new BufferedInputStream (new FileInputStream (f), BUFFERSIZE);
        String en = ""META-INF"" + ""/"" + ""MANIFEST.MF"";
        out.putNextEntry (new ZipEntry (en));
        while ((bytes_read = in.read (buffer)) != - 1) {
            out.write (buffer, 0, bytes_read);
        }
        in.close ();
        out.closeEntry ();
    } catch (Exception e) {
        System.out.println (""[writeManifestEntry(), JarWriter] ERROR\n"" + e);
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
6368468,"boolean copyFileStructure (File oldFile, File newFile) {
    if (oldFile == null || newFile == null) return false;

    File searchFile = newFile;
    do {
        if (oldFile.equals (searchFile)) return false;

        searchFile = searchFile.getParentFile ();
    } while (searchFile != null);
    if (oldFile.isDirectory ()) {
        if (progressDialog != null) {
            progressDialog.setDetailFile (oldFile, ProgressDialog.COPY);
        }
        if (simulateOnly) {
        } else {
            if (! newFile.mkdirs ()) return false;

        }
        File [] subFiles = oldFile.listFiles ();
        if (subFiles != null) {
            if (progressDialog != null) {
                progressDialog.addWorkUnits (subFiles.length);
            }
            for (int i = 0;
            i < subFiles.length; i ++) {
                File oldSubFile = subFiles [i];
                File newSubFile = new File (newFile, oldSubFile.getName ());
                if (! copyFileStructure (oldSubFile, newSubFile)) return false;

                if (progressDialog != null) {
                    progressDialog.addProgress (1);
                    if (progressDialog.isCancelled ()) return false;

                }
            }
        }
    } else {
        if (simulateOnly) {
        } else {
            FileReader in = null;
            FileWriter out = null;
            try {
                in = new FileReader (oldFile);
                out = new FileWriter (newFile);
                int count;
                while ((count = in.read ()) != - 1) out.write (count);

            } catch (FileNotFoundException e) {
                return false;
            } catch (IOException e) {
                return false;
            } finally {
                try {
                    if (in != null) in.close ();

                    if (out != null) out.close ();

                } catch (IOException e) {
                    return false;
                }
            }
        }
    }
    return true;
}
",8625346,"public static boolean encodeFileToFile (String infile, String outfile) {
    boolean success = false;
    java.io.InputStream in = null;
    java.io.OutputStream out = null;
    try {
        in = new Base64.InputStream (new java.io.BufferedInputStream (new java.io.FileInputStream (infile)), Base64.ENCODE);
        out = new java.io.BufferedOutputStream (new java.io.FileOutputStream (outfile));
        byte [] buffer = new byte [65536];
        int read = - 1;
        while ((read = in.read (buffer)) >= 0) {
            out.write (buffer, 0, read);
        }
        success = true;
    } catch (java.io.IOException exc) {
        exc.printStackTrace ();
    } finally {
        try {
            in.close ();
        } catch (Exception exc) {
        }
        try {
            out.close ();
        } catch (Exception exc) {
        }
    }
    return success;
}
",Copy File,Type-3 (WT3/4),TRUE
1514106,"private void exportLearningUnitView (File selectedFile) {
    if (learningUnitViewElementsManager.isOriginalElementsOnly ()) {
        String [] elementIds = learningUnitViewElementsManager.getAllLearningUnitViewElementIds ();
        for (int i = 0;
        i < elementIds.length; i ++) {
            FSLLearningUnitViewElement element = learningUnitViewElementsManager.getLearningUnitViewElement (elementIds [i], false);
            if (element.getLastModificationDate () == null) {
                element.setLastModificationDate (String.valueOf (new Date ().getTime ()));
                element.setModified (true);
            }
        }
        learningUnitViewElementsManager.setModified (true);
        learningUnitViewManager.saveLearningUnitViewData ();
        if (selectedFile != null) {
            try {
                File outputFile = selectedFile;
                String fileName = outputFile.getName ();
                StringBuffer extension = new StringBuffer ();
                if (fileName.length () >= 5) {
                    for (int i = 5;
                    i > 0; i --) {
                        extension.append (fileName.charAt (fileName.length () - i));
                    }
                }
                if (! extension.toString ().equals ("".fslv"")) {
                    outputFile.renameTo (new File (outputFile.getAbsolutePath () + "".fslv""));
                    outputFile = new File (outputFile.getAbsolutePath () + "".fslv"");
                }
                File files [] = selectedFile.getParentFile ().listFiles ();
                int returnValue = FLGOptionPane.OK_OPTION;
                for (int i = 0;
                i < files.length; i ++) {
                    if (outputFile.getAbsolutePath ().equals (files [i].getAbsolutePath ())) {
                        returnValue = FLGOptionPane.showConfirmDialog (internationalization.getString (""dialog.exportLearningUnitView.fileExits.message""), internationalization.getString (""dialog.exportLearningUnitView.fileExits.title""), FLGOptionPane.OK_CANCEL_OPTION, FLGOptionPane.QUESTION_MESSAGE);
                        break;
                    }
                }
                if (returnValue == FLGOptionPane.OK_OPTION) {
                    FileOutputStream os = new FileOutputStream (outputFile);
                    ZipOutputStream zipOutputStream = new ZipOutputStream (os);
                    ZipEntry zipEntry = new ZipEntry (""dummy"");
                    zipOutputStream.putNextEntry (zipEntry);
                    zipOutputStream.closeEntry ();
                    zipOutputStream.flush ();
                    zipOutputStream.finish ();
                    zipOutputStream.close ();
                    final File outFile = outputFile;
                    (new Thread () {
                        public void run () {
                            try {
                                ZipOutputStream zipOutputStream = new ZipOutputStream (new FileOutputStream (outFile));
                                File [] files = (new File (learningUnitViewManager.getLearningUnitViewOriginalDataDirectory ().getPath ())).listFiles ();
                                int maxSteps = files.length;
                                int step = 1;
                                exportProgressDialog = new FLGImageProgressDialog (null, 0, maxSteps, 0, getClass ().getClassLoader ().getResource (""freestyleLearning/homeCore/images/fsl.gif""), (Color) UIManager.get (""FSLColorBlue""), (Color) UIManager.get (""FSLColorRed""), internationalization.getString (""learningUnitViewExport.rogressbarText""));
                                exportProgressDialog.setCursor (new Cursor (Cursor.WAIT_CURSOR));
                                exportProgressDialog.setBarValue (step);
                                buildExportZipFile ("""", zipOutputStream, files, step);
                                zipOutputStream.flush ();
                                zipOutputStream.finish ();
                                zipOutputStream.close ();
                                exportProgressDialog.setBarValue (maxSteps);
                                exportProgressDialog.setCursor (new Cursor (Cursor.DEFAULT_CURSOR));
                                exportProgressDialog.dispose ();
                            } catch (Exception e) {
                                e.printStackTrace ();
                            }
                        }}

                    ).start ();
                    os.close ();
                }
            } catch (Exception exp) {
                exp.printStackTrace ();
            }
        }
    } else {
    }
}
",7577030,"private void zipFiles (File file, File [] fa) throws Exception {
    File f = new File (file, ALL_FILES_NAME);
    if (f.exists ()) {
        f.delete ();
        f = new File (file, ALL_FILES_NAME);
    }
    ZipOutputStream zoutstrm = new ZipOutputStream (new FileOutputStream (f));
    for (int i = 0;
    i < fa.length; i ++) {
        ZipEntry zipEntry = new ZipEntry (fa [i].getName ());
        zoutstrm.putNextEntry (zipEntry);
        FileInputStream fr = new FileInputStream (fa [i]);
        byte [] buffer = new byte [1024];
        int readCount = 0;
        while ((readCount = fr.read (buffer)) > 0) {
            zoutstrm.write (buffer, 0, readCount);
        }
        fr.close ();
        zoutstrm.closeEntry ();
    }
    zoutstrm.close ();
    log (""created zip file: "" + file.getName () + ""/"" + ALL_FILES_NAME);
}
",Zip Files,Type-3 (WT3/4),FALSE
1579007,"private void nextZipEntry (String url, int level) throws IOException {
    if (! url.startsWith (""META-INF/"") && ! url.startsWith (""OEBPS/"")) url = ""OEBPS/"" + url;

    ZipEntry ze = new ZipEntry (url);
    ze.setMethod (ZipEntry.DEFLATED);
    tmpzos.putNextEntry (ze);
}
",22055554,"protected void addFileToJar (JarOutputStream jStream, File inputFile, String logicalFilename) throws BuildException {
    FileInputStream iStream = null;
    try {
        if (! addedfiles.contains (logicalFilename)) {
            iStream = new FileInputStream (inputFile);
            ZipEntry zipEntry = new ZipEntry (logicalFilename.replace ('\\', '/'));
            jStream.putNextEntry (zipEntry);
            byte [] byteBuffer = new byte [2 * DEFAULT_BUFFER_SIZE];
            int count = 0;
            do {
                jStream.write (byteBuffer, 0, count);
                count = iStream.read (byteBuffer, 0, byteBuffer.length);
            } while (count != - 1);
            addedfiles.add (logicalFilename);
        }
    } catch (IOException ioe) {
        log (""WARNING: IOException while adding entry "" + logicalFilename + "" to jarfile from "" + inputFile.getPath () + "" "" + ioe.getClass ().getName () + ""-"" + ioe.getMessage (), Project.MSG_WARN);
    } finally {
        if (iStream != null) {
            try {
                iStream.close ();
            } catch (IOException closeException) {
            }
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
9275622,"private boolean copyFile (File _file1, File _file2) {
    FileInputStream fis;
    FileOutputStream fos;
    try {
        fis = new FileInputStream (_file1);
        fos = new FileOutputStream (_file2);
        FileChannel canalFuente = fis.getChannel ();
        canalFuente.transferTo (0, canalFuente.size (), fos.getChannel ());
        fis.close ();
        fos.close ();
        return true;
    } catch (FileNotFoundException e) {
    } catch (IOException e) {
    }
    return false;
}
",12312915,"public static void entering (String [] args) throws IOException, CodeCheckException {
    ClassWriter writer = new ClassWriter ();
    writer.readClass (new BufferedInputStream (new FileInputStream (args [0])));
    int constantIndex = writer.getStringConstantIndex (""Entering "");
    int fieldRefIndex = writer.getReferenceIndex (ClassWriter.CONSTANT_Fieldref, ""java/lang/System"", ""out"", ""Ljava/io/PrintStream;"");
    int printlnRefIndex = writer.getReferenceIndex (ClassWriter.CONSTANT_Methodref, ""java/io/PrintStream"", ""println"", ""(Ljava/lang/String;)V"");
    int printRefIndex = writer.getReferenceIndex (ClassWriter.CONSTANT_Methodref, ""java/io/PrintStream"", ""print"", ""(Ljava/lang/String;)V"");
    for (Iterator i = writer.getMethods ().iterator ();
    i.hasNext ();) {
        MethodInfo method = (MethodInfo) i.next ();
        if (method.getName ().equals (""readConstant"")) continue;

        CodeAttribute attribute = method.getCodeAttribute ();
        ArrayList instructions = new ArrayList (10);
        byte [] operands;
        operands = new byte [2];
        NetByte.intToPair (fieldRefIndex, operands, 0);
        instructions.add (new Instruction (OpCode.getOpCodeByMnemonic (""getstatic""), 0, operands, false));
        instructions.add (new Instruction (OpCode.getOpCodeByMnemonic (""dup""), 0, null, false));
        instructions.add (Instruction.appropriateLdc (constantIndex, false));
        operands = new byte [2];
        NetByte.intToPair (printRefIndex, operands, 0);
        instructions.add (new Instruction (OpCode.getOpCodeByMnemonic (""invokevirtual""), 0, operands, false));
        instructions.add (Instruction.appropriateLdc (writer.getStringConstantIndex (method.getName ()), false));
        operands = new byte [2];
        NetByte.intToPair (printlnRefIndex, operands, 0);
        instructions.add (new Instruction (OpCode.getOpCodeByMnemonic (""invokevirtual""), 0, operands, false));
        attribute.insertInstructions (0, 0, instructions);
        attribute.codeCheck ();
    }
    BufferedOutputStream outStream = new BufferedOutputStream (new FileOutputStream (args [1]));
    writer.writeClass (outStream);
    outStream.close ();
}
",Copy File,Type-3 (WT3/4),TRUE
418257,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",10620258,"private void writeFileToZip (ZipOutputStream out, String sourceFilename, String vPath) throws IOException {
    FileInputStream in = new FileInputStream (sourceFilename);
    out.putNextEntry (new ZipEntry (vPath));
    int len;
    byte [] buf = new byte [1024];
    while ((len = in.read (buf)) > 0) {
        out.write (buf, 0, len);
    }
    out.closeEntry ();
    in.close ();
}
",Zip Files,Type-3 (WT3/4),FALSE
268806,"public void convert (File src, File dest) throws IOException {
    InputStream in = new BufferedInputStream (new FileInputStream (src));
    DcmParser p = pfact.newDcmParser (in);
    Dataset ds = fact.newDataset ();
    p.setDcmHandler (ds.getDcmHandler ());
    try {
        FileFormat format = p.detectFileFormat ();
        if (format != FileFormat.ACRNEMA_STREAM) {
            System.out.println (""\n"" + src + "": not an ACRNEMA stream!"");
            return;
        }
        p.parseDcmFile (format, Tags.PixelData);
        if (ds.contains (Tags.StudyInstanceUID) || ds.contains (Tags.SeriesInstanceUID) || ds.contains (Tags.SOPInstanceUID) || ds.contains (Tags.SOPClassUID)) {
            System.out.println (""\n"" + src + "": contains UIDs!"" + "" => probable already DICOM - do not convert"");
            return;
        }
        boolean hasPixelData = p.getReadTag () == Tags.PixelData;
        boolean inflate = hasPixelData && ds.getInt (Tags.BitsAllocated, 0) == 12;
        int pxlen = p.getReadLength ();
        if (hasPixelData) {
            if (inflate) {
                ds.putUS (Tags.BitsAllocated, 16);
                pxlen = pxlen * 4 / 3;
            }
            if (pxlen != (ds.getInt (Tags.BitsAllocated, 0)>>> 3) * ds.getInt (Tags.Rows, 0) * ds.getInt (Tags.Columns, 0) * ds.getInt (Tags.NumberOfFrames, 1) * ds.getInt (Tags.NumberOfSamples, 1)) {
                System.out.println (""\n"" + src + "": mismatch pixel data length!"" + "" => do not convert"");
                return;
            }
        }
        ds.putUI (Tags.StudyInstanceUID, uid (studyUID));
        ds.putUI (Tags.SeriesInstanceUID, uid (seriesUID));
        ds.putUI (Tags.SOPInstanceUID, uid (instUID));
        ds.putUI (Tags.SOPClassUID, classUID);
        if (! ds.contains (Tags.NumberOfSamples)) {
            ds.putUS (Tags.NumberOfSamples, 1);
        }
        if (! ds.contains (Tags.PhotometricInterpretation)) {
            ds.putCS (Tags.PhotometricInterpretation, ""MONOCHROME2"");
        }
        if (fmi) {
            ds.setFileMetaInfo (fact.newFileMetaInfo (ds, UIDs.ImplicitVRLittleEndian));
        }
        OutputStream out = new BufferedOutputStream (new FileOutputStream (dest));
        try {
        } finally {
            ds.writeFile (out, encodeParam ());
            if (hasPixelData) {
                if (! skipGroupLen) {
                    out.write (PXDATA_GROUPLEN);
                    int grlen = pxlen + 8;
                    out.write ((byte) grlen);
                    out.write ((byte) (grlen>> 8));
                    out.write ((byte) (grlen>> 16));
                    out.write ((byte) (grlen>> 24));
                }
                out.write (PXDATA_TAG);
                out.write ((byte) pxlen);
                out.write ((byte) (pxlen>> 8));
                out.write ((byte) (pxlen>> 16));
                out.write ((byte) (pxlen>> 24));
            }
            if (inflate) {
                int b2, b3;
                for (; pxlen > 0; pxlen -= 3) {
                    out.write (in.read ());
                    b2 = in.read ();
                    b3 = in.read ();
                    out.write (b2 & 0x0f);
                    out.write (b2>> 4 | ((b3 & 0x0f) << 4));
                    out.write (b3>> 4);
                }
            } else {
                for (; pxlen > 0; -- pxlen) {
                    out.write (in.read ());
                }
            }
            out.close ();
        }
        System.out.print ('.');
    } finally {
        in.close ();
    }
}
",17296395,"public static File copyToLibDirectory (final File file) throws FileNotFoundException, IOException {
    if (file == null || ! file.exists ()) {
        throw new FileNotFoundException ();
    }
    File directory = new File (""lib/"");
    File dest = new File (directory, file.getName ());
    File parent = dest.getParentFile ();
    while (parent != null && ! parent.equals (directory)) {
        parent = parent.getParentFile ();
    }
    if (parent.equals (directory)) {
        return file;
    }
    FileChannel in = null;
    FileChannel out = null;
    try {
        in = new FileInputStream (file).getChannel ();
        out = new FileOutputStream (dest).getChannel ();
        in.transferTo (0, in.size (), out);
    } finally {
        if (in != null) {
            try {
                in.close ();
            } catch (IOException e) {
            }
        }
        if (out != null) {
            try {
                out.close ();
            } catch (IOException e) {
            }
        }
    }
    return dest;
}
",Copy File,Type-3 (WT3/4),TRUE
418257,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",23309807,"public OCFContainerWriter (OutputStream out, String mime) throws IOException {
    zip = new ZipOutputStream (out);
    try {
        byte [] bytes = mime.getBytes (""UTF-8"");
        ZipEntry mimetype = new ZipEntry (""mimetype"");
        mimetype.setMethod (ZipOutputStream.STORED);
        mimetype.setSize (bytes.length);
        mimetype.setCompressedSize (bytes.length);
        CRC32 crc = new CRC32 ();
        crc.update (bytes);
        mimetype.setCrc (crc.getValue ());
        zip.putNextEntry (mimetype);
        zip.write (bytes);
        zip.closeEntry ();
    } catch (UnsupportedEncodingException e) {
        e.printStackTrace ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
2049240,"private void writeInfos () throws IOException {
    zos.putNextEntry (new ZipEntry (""info.bin""));
    outFile = new DataOutputStream (zos);
    outFile.writeInt (VERSION);
    outFile.writeInt (MINORVERSION);
    outFile.writeDouble (intervall_s);
    zos.closeEntry ();
}
",22572311,"public static byte [] zipFiles (Map < String, byte [] > files) throws IOException {
    ByteArrayOutputStream dest = new ByteArrayOutputStream ();
    ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest));
    Iterator < Entry < String, byte [] > > itr = files.entrySet ().iterator ();
    while (itr.hasNext ()) {
        Entry < String, byte [] > entry = itr.next ();
        ZipEntry zipEntry = new ZipEntry (entry.getKey ());
        out.putNextEntry (zipEntry);
        IOUtils.write (entry.getValue (), out);
    }
    out.close ();
    byte [] outBytes = dest.toByteArray ();
    dest.close ();
    return outBytes;
}
",Zip Files,Type-3 (WT3/4),FALSE
3266833,"public MotixFileItem (final InputStream is, final String name, final String contentType, final int index) throws IOException {
    this.name = name;
    this.contentType = contentType;
    this.index = index;
    this.extension = FilenameUtils.getExtension (this.name);
    this.isImage = ImageUtils.isImage (name);
    ArrayInputStream isAux = null;
    final ByteArrayOutputStream out = new ByteArrayOutputStream ();
    try {
        IOUtils.copy (is, out);
        isAux = new ArrayInputStream (out.toByteArray ());
        if (this.isImage) {
            this.bufferedImage = imaging.read (isAux);
        }
    } finally {
        IOUtils.closeQuietly (out);
        IOUtils.closeQuietly (isAux);
    }
    this.inputStream = new ArrayInputStream (out.toByteArray ());
}
",18400649,"public static void copyFiles (String strPath, String dstPath) throws IOException {
    File src = new File (strPath);
    File dest = new File (dstPath);
    if (src.isDirectory ()) {
        dest.mkdirs ();
        String list [] = src.list ();
        for (int i = 0;
        i < list.length; i ++) {
            if (list [i].lastIndexOf (SVN) != - 1) {
                if (! SVN.equalsIgnoreCase (list [i].substring (list [i].length () - 4, list [i].length ()))) {
                    String dest1 = dest.getAbsolutePath () + ""\\"" + list [i];
                    String src1 = src.getAbsolutePath () + ""\\"" + list [i];
                    copyFiles (src1, dest1);
                }
            } else {
                String dest1 = dest.getAbsolutePath () + ""\\"" + list [i];
                String src1 = src.getAbsolutePath () + ""\\"" + list [i];
                copyFiles (src1, dest1);
            }
        }
    } else {
        FileInputStream fin = new FileInputStream (src);
        FileOutputStream fout = new FileOutputStream (dest);
        int c;
        while ((c = fin.read ()) >= 0) fout.write (c);

        fin.close ();
        fout.close ();
    }
}
",Copy File,Type-3 (WT3/4),TRUE
7209802,"public static void main (String [] args) throws IOException {
    ServerSocket serverSocket = null;
    try {
        serverSocket = new ServerSocket (4444);
    } catch (IOException e) {
        System.err.println (""Could not listen on port: 4444."");
        System.exit (1);
    }
    Socket clientSocket = null;
    try {
        clientSocket = serverSocket.accept ();
    } catch (IOException e) {
        System.err.println (""Accept failed."");
        System.exit (1);
    }
    DataOutputStream out = new DataOutputStream (clientSocket.getOutputStream ());
    BufferedReader in = new BufferedReader (new InputStreamReader (clientSocket.getInputStream ()));
    String inputLine, outputLine;
    inputLine = in.readLine ();
    String dist_metric = in.readLine ();
    File outFile = new File (""data.txt"");
    FileWriter outw = new FileWriter (outFile);
    outw.write (inputLine);
    outw.close ();
    File sample_coords = new File (""sample_coords.txt"");
    sample_coords.delete ();
    File sp_coords = new File (""sp_coords.txt"");
    sp_coords.delete ();
    try {
        System.out.println (""Running python script..."");
        System.out.println (""Command: "" + ""python l19test.py "" + ""\"""" + dist_metric + ""\"""");
        Process pr = Runtime.getRuntime ().exec (""python l19test.py "" + dist_metric);
        BufferedReader br = new BufferedReader (new InputStreamReader (pr.getErrorStream ()));
        String line;
        while ((line = br.readLine ()) != null) {
            System.out.println (line);
        }
        int exitVal = pr.waitFor ();
        System.out.println (""Process Exit Value: "" + exitVal);
        System.out.println (""done."");
    } catch (Exception e) {
        System.out.println (""Unable to run python script for PCoA analysis"");
    }
    File myFile = new File (""sp_coords.txt"");
    byte [] mybytearray = new byte [(new Long (myFile.length ())).intValue ()];
    FileInputStream fis = new FileInputStream (myFile);
    System.out.println (""."");
    System.out.println (myFile.length ());
    out.writeInt ((int) myFile.length ());
    for (int i = 0;
    i < myFile.length (); i ++) {
        out.writeByte (fis.read ());
    }
    myFile = new File (""sample_coords.txt"");
    mybytearray = new byte [(int) myFile.length ()];
    fis = new FileInputStream (myFile);
    fis.read (mybytearray);
    System.out.println (""."");
    System.out.println (myFile.length ());
    out.writeInt ((int) myFile.length ());
    out.write (mybytearray);
    myFile = new File (""evals.txt"");
    mybytearray = new byte [(new Long (myFile.length ())).intValue ()];
    fis = new FileInputStream (myFile);
    fis.read (mybytearray);
    System.out.println (""."");
    System.out.println (myFile.length ());
    out.writeInt ((int) myFile.length ());
    out.write (mybytearray);
    out.flush ();
    out.close ();
    in.close ();
    clientSocket.close ();
    serverSocket.close ();
}
",12440171,"public void writeFile (String resource, InputStream is) throws IOException {
    File f = prepareFsReferenceAsFile (resource);
    FileOutputStream fos = new FileOutputStream (f);
    BufferedOutputStream bos = new BufferedOutputStream (fos);
    try {
        IOUtils.copy (is, bos);
    } finally {
        IOUtils.closeQuietly (is);
        IOUtils.closeQuietly (bos);
    }
}
",Copy File,Type-3 (WT3/4),TRUE
12819863,"public static String generatePassword (String userKey, int applicationId, String applicationKey) {
    String nonce = generateNonce ();
    String createDate = fmtDate.format (new Date ());
    String keyDigest = null;
    MessageDigest sha1 = null;
    try {
        sha1 = MessageDigest.getInstance (""SHA1"");
        sha1.update (nonce.getBytes (""UTF-8""));
        sha1.update (createDate.getBytes (""UTF-8""));
        sha1.update (userKey.getBytes (""UTF-8""));
        sha1.update (applicationKey.getBytes (""UTF-8""));
        keyDigest = getHexaDecimal (sha1.digest ());
    } catch (Exception e) {
        throw new RuntimeException (e);
    }
    StringBuilder sb = new StringBuilder ();
    sb.append (applicationId);
    sb.append (',');
    sb.append (nonce);
    sb.append (',');
    sb.append (createDate);
    sb.append (',');
    sb.append (keyDigest);
    return sb.toString ();
}
",22915885,"public Login authenticateClient () {
    Object o;
    String user, password;
    Vector < Login > clientLogins = ClientLoginsTableModel.getClientLogins ();
    Login login = null;
    try {
        socket.setSoTimeout (25000);
        objectOut.writeObject (""JFRITZ SERVER 1.1"");
        objectOut.flush ();
        o = objectIn.readObject ();
        if (o instanceof String) {
            user = (String) o;
            objectOut.flush ();
            for (Login l : clientLogins) {
                if (l.getUser ().equals (user)) {
                    login = l;
                    break;
                }
            }
            if (login != null) {
                MessageDigest md = MessageDigest.getInstance (""MD5"");
                md.update (login.getPassword ().getBytes ());
                DESKeySpec desKeySpec = new DESKeySpec (md.digest ());
                SecretKeyFactory keyFactory = SecretKeyFactory.getInstance (""DES"");
                SecretKey secretKey = keyFactory.generateSecret (desKeySpec);
                Cipher desCipher = Cipher.getInstance (""DES/ECB/PKCS5Padding"");
                desCipher.init (Cipher.ENCRYPT_MODE, secretKey);
                byte [] dataKeySeed = new byte [32];
                Random random = new Random ();
                random.nextBytes (dataKeySeed);
                md.reset ();
                md.update (dataKeySeed);
                dataKeySeed = md.digest ();
                SealedObject dataKeySeedSealed;
                dataKeySeedSealed = new SealedObject (dataKeySeed, desCipher);
                objectOut.writeObject (dataKeySeedSealed);
                objectOut.flush ();
                desKeySpec = new DESKeySpec (dataKeySeed);
                secretKey = keyFactory.generateSecret (desKeySpec);
                inCipher = Cipher.getInstance (""DES/ECB/PKCS5Padding"");
                outCipher = Cipher.getInstance (""DES/ECB/PKCS5Padding"");
                inCipher.init (Cipher.DECRYPT_MODE, secretKey);
                outCipher.init (Cipher.ENCRYPT_MODE, secretKey);
                SealedObject sealedObject = (SealedObject) objectIn.readObject ();
                o = sealedObject.getObject (inCipher);
                if (o instanceof String) {
                    String response = (String) o;
                    if (response.equals (""OK"")) {
                        SealedObject ok_sealed = new SealedObject (""OK"", outCipher);
                        objectOut.writeObject (ok_sealed);
                        return login;
                    } else {
                        Debug.netMsg (""Client sent false response to challenge!"");
                    }
                } else {
                    Debug.netMsg (""Client sent false object as response to challenge!"");
                }
            } else {
                Debug.netMsg (""client sent unkown username: "" + user);
            }
        }
    } catch (IllegalBlockSizeException e) {
        Debug.netMsg (""Wrong blocksize for sealed object!"");
        Debug.error (e.toString ());
        e.printStackTrace ();
    } catch (ClassNotFoundException e) {
        Debug.netMsg (""received unrecognized object from client!"");
        Debug.error (e.toString ());
        e.printStackTrace ();
    } catch (NoSuchAlgorithmException e) {
        Debug.netMsg (""MD5 Algorithm not present in this JVM!"");
        Debug.error (e.toString ());
        e.printStackTrace ();
    } catch (InvalidKeySpecException e) {
        Debug.netMsg (""Error generating cipher, problems with key spec?"");
        Debug.error (e.toString ());
        e.printStackTrace ();
    } catch (InvalidKeyException e) {
        Debug.netMsg (""Error genertating cipher, problems with key?"");
        Debug.error (e.toString ());
        e.printStackTrace ();
    } catch (NoSuchPaddingException e) {
        Debug.netMsg (""Error generating cipher, problems with padding?"");
        Debug.error (e.toString ());
        e.printStackTrace ();
    } catch (IOException e) {
        Debug.netMsg (""Error authenticating client!"");
        Debug.error (e.toString ());
        e.printStackTrace ();
    } catch (BadPaddingException e) {
        Debug.netMsg (""Bad padding exception!"");
        Debug.error (e.toString ());
        e.printStackTrace ();
    }
    return null;
}
",Secure Hash,Type-3 (WT3/4),TRUE
891054,"public Thread transmitThread (final Socket s, final CountDownLatch abortLatch) {
    final Thread theThread = new Thread () {
        @Override
        public void run () {
            final Random r = new Random ();
            final Counter counter = new Counter (""TRANSMIT"", plotter);
            counter.start ();
            try {
                final DataOutputStream dos = new DataOutputStream (new BufferedOutputStream (s.getOutputStream ()));
                while (! Thread.interrupted ()) {
                    if (! running.get ()) {
                        Thread.sleep (1000);
                        continue;
                    }
                    final int packetSize = r.nextInt (8192) + 2048;
                    final byte [] packet = new byte [packetSize];
                    r.nextBytes (packet);
                    final CRC32 crc = new CRC32 ();
                    crc.update (packet);
                    dos.writeInt (packetSize);
                    counter.addBytes (INTEGER_BYTES);
                    dos.write (packet);
                    counter.addBytes (packetSize);
                    dos.writeLong (crc.getValue ());
                    counter.addBytes (CRC_BYTES);
                    dos.flush ();
                }
            } catch (InterruptedException e) {
                System.out.println (""Transmitter thread interrupted!"");
            } catch (Exception e) {
                System.err.println (""Unexpected error in transmitter thread: "" + e.getMessage ());
            } finally {
                abortLatch.countDown ();
                counter.interrupt ();
            }
        }}

    ;
    return theThread;
}
",1302030,"private static String getUnicodeStringIfOriginalMatches (AbstractUnicodeExtraField f, byte [] orig) {
    if (f != null) {
        CRC32 crc32 = new CRC32 ();
        crc32.update (orig);
        long origCRC32 = crc32.getValue ();
        if (origCRC32 == f.getNameCRC32 ()) {
            try {
                return ZipEncodingHelper.UTF8_ZIP_ENCODING.decode (f.getUnicodeName ());
            } catch (IOException ex) {
                return null;
            }
        }
    }
    return null;
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
16319456,"@Override
public List < SectionFinderResult > lookForSections (String text, Section < ? > father, Type type) {
    ArrayList < SectionFinderResult > result = new ArrayList < SectionFinderResult > ();
    Pattern TABLE_LINE = Pattern.compile (TABLE_LINE_REGEXP, Pattern.MULTILINE);
    Matcher m = TABLE_LINE.matcher (text);
    int end = 0;
    int tableStart = - 1;
    int tableEnd = - 1;
    while (m.find (end)) {
        int start = m.start ();
        end = m.end ();
        if (tableEnd == start) {
            tableEnd = end;
        } else {
            addResultIfAvailable (result, tableStart, tableEnd);
            tableStart = start;
            tableEnd = end;
        }
        if (end >= text.length ()) break;

    }
    addResultIfAvailable (result, tableStart, tableEnd);
    return result;
}
",19047757,"public LinkedList < SearchResult > search (String strRequest) {
    LinkedList < SearchResult > ret = new LinkedList < SearchResult > ();
    HttpClient h = new HttpClient ();
    try {
        String strRequestUrl = ""http://www.youporn.com/search"";
        if (strRequest.toLowerCase ().contains (""straight!"")) {
            strRequestUrl += ""?type=straight"";
            strRequest = strRequest.replaceAll (""straight!"", """");
        }
        if (strRequest.toLowerCase ().contains (""gay!"")) {
            strRequestUrl += ""?type=gay"";
            strRequest = strRequest.replaceAll (""gay!"", """");
        }
        if (strRequest.toLowerCase ().contains (""cocks!"")) {
            strRequestUrl += ""?type=cocks"";
            strRequest = strRequest.replaceAll (""cocks!"", """");
        }
        if (! strRequestUrl.endsWith (""search"")) strRequestUrl += ""&"";
        else strRequestUrl += ""?"";

        strRequestUrl += ""query="" + URLEncoder.encode (strRequest, ""UTF-8"");
        if (NoMuleRuntime.DEBUG) System.out.println (strRequestUrl);

        GetMethod get = new GetMethod (strRequestUrl);
        Date d = new Date ((new Date ()).getTime () + (1 * 24 * 3600 * 1000));
        h.getState ().addCookie (new Cookie ("".youporn.com"", ""age_check"", ""1"", ""/"", d, false));
        h.executeMethod (get);
        BufferedReader in = new BufferedReader (new InputStreamReader (get.getResponseBodyAsStream ()));
        String s = """";
        String res = """";
        while ((s = in.readLine ()) != null) {
            res += s;
        }
        get.releaseConnection ();
        if (NoMuleRuntime.DEBUG) System.out.println (res);

        String regexp = ""\\<a href\\=\""\\/watch\\/[^\""]+\""\\>[^\\<]+"";
        Pattern p = Pattern.compile (regexp);
        Matcher m = p.matcher (res);
        while (m.find ()) {
            int startPos = m.start () + ""<a href=\"""".length ();
            String strUrl = ""http://www.youporn.com"";
            int pos = 0;
            for (pos = startPos; pos < m.end () && (res.charAt (pos) != '\""'); pos ++) {
                strUrl += res.charAt (pos);
            }
            String strTitle = res.substring (pos + 2, m.end ());
            if (strTitle.trim ().length () > 0) ret.add (new SearchResult (strTitle + "" at YouPorn"", strUrl));

        }
        return ret;
    } catch (UnsupportedEncodingException e) {
        e.printStackTrace ();
    } catch (HttpException e) {
        e.printStackTrace ();
    } catch (IOException e) {
        e.printStackTrace ();
    }
    return null;
}
",Extract Matches Using Regex,Type-3 (WT3/4),TRUE
7990229,"public static InputStream gunzip (final InputStream inputStream) throws IOException {
    Assert.notNull (inputStream, ""inputStream"");
    GZIPInputStream gzipInputStream = new GZIPInputStream (inputStream);
    InputOutputStream inputOutputStream = new InputOutputStream ();
    IOUtils.copy (gzipInputStream, inputOutputStream);
    return inputOutputStream.getInputStream ();
}
",15520770,"public void writeConfigurationFile () throws IOException, ComponentException {
    SystemConfig config = parent.getParentSystem ().getConfiguration ();
    File original = config.getLocation ();
    File backup = new File (original.getParentFile (), original.getName () + ""."" + System.currentTimeMillis ());
    FileInputStream in = new FileInputStream (original);
    FileOutputStream out = new FileOutputStream (backup);
    byte [] buffer = new byte [2048];
    try {
        int bytesread = 0;
        while ((bytesread = in.read (buffer)) > 0) {
            out.write (buffer, 0, bytesread);
        }
    } catch (IOException e) {
        logger.warn (""Failed to copy backup of configuration file"");
        throw e;
    } finally {
        in.close ();
        out.close ();
    }
    FileWriter replace = new FileWriter (original);
    replace.write (config.toFileFormat ());
    replace.close ();
    logger.info (""Re-wrote configuration file "" + original.getPath ());
}
",Copy File,Type-3 (WT3/4),TRUE
1086128,"public void streamDataToZip (VolumeTimeSeries vol, ZipOutputStream zout) throws Exception {
    ZipEntry entry = new ZipEntry (vol.getId () + "".dat"");
    zout.putNextEntry (entry);
    if (vol instanceof FloatVolumeTimeSeries) {
        streamData (((FloatVolumeTimeSeries) vol).getData (), zout);
    } else if (vol instanceof RGBVolumeTimeSeries) {
        streamData (((RGBVolumeTimeSeries) vol).getARGBData (), zout);
    } else if (vol instanceof BinaryVolumeTimeSeries) {
        streamData (((BinaryVolumeTimeSeries) vol).getBinaryData (), zout);
    }

}
",13374130,"private void zipLog (InfoRolling info) {
    boolean zipped = false;
    File [] logFiles = info.getFiles ();
    try {
        GregorianCalendar gc = (GregorianCalendar) GregorianCalendar.getInstance ();
        gc.roll (Calendar.DAY_OF_MONTH, info.getBackRolling ());
        final String prefixFileName = logFileName.substring (0, logFileName.indexOf ("".""));
        final String date = sdf.format (gc.getTime ());
        String tarName = new StringBuffer (prefixFileName).append (date).append ("".tar"").toString ();
        String gzipFileName = new StringBuffer (tarName).append ("".zip"").toString ();
        String tarPath = new StringBuffer (logDir).append (File.separator).append (tarName).toString ();
        TarArchive ta = new TarArchive (new FileOutputStream (tarPath));
        for (int i = 0;
        i < logFiles.length; i ++) {
            File file = logFiles [i];
            TarEntry te = new TarEntry (file);
            ta.writeEntry (te, true);
        }
        ta.closeArchive ();
        ZipEntry zipEntry = new ZipEntry (tarName);
        zipEntry.setMethod (ZipEntry.DEFLATED);
        ZipOutputStream zout = new ZipOutputStream (new FileOutputStream (new StringBuffer (logDir).append (File.separator).append (gzipFileName).toString ()));
        zout.putNextEntry (zipEntry);
        InputStream in = new FileInputStream (tarPath);
        byte [] buffer = new byte [2048];
        int ch = 0;
        while ((ch = in.read (buffer)) >= 0) {
            zout.write (buffer, 0, ch);
        }
        zout.flush ();
        zout.close ();
        in.close ();
        logFiles = new File (getFile ().substring (0, getFile ().lastIndexOf (File.separator))).listFiles (new FileFilter () {
            public boolean accept (File file) {
                return file.getName ().endsWith ("".tar"");
            }}

        );
        for (int i = 0;
        i < logFiles.length; i ++) {
            File file = logFiles [i];
            System.out.println (""cancello : "" + file.getAbsolutePath () + "" : "" + file.delete ());
        }
        logFiles = new File (getFile ().substring (0, getFile ().lastIndexOf (File.separator))).listFiles (new FileFilter () {
            public boolean accept (File file) {
                return file.getName ().indexOf (prefixFileName + "".log"" + date) != - 1 && ! file.getName ().endsWith ("".zip"");
            }}

        );
        for (int i = 0;
        i < logFiles.length; i ++) {
            File file = logFiles [i];
            System.out.println (""cancello : "" + file.getAbsolutePath () + "" : "" + file.delete ());
        }
        zipped = true;
    } catch (FileNotFoundException ex) {
        LogLog.error (""Filenotfound: "" + ex.getMessage (), ex);
    } catch (IOException ex) {
        LogLog.error (""IOException: "" + ex.getMessage (), ex);
    } finally {
        if (zipped) {
            for (int i = 0;
            i < logFiles.length; i ++) {
                File file = logFiles [i];
                file.delete ();
            }
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
9371509,"public SWORDEntry ingestDepost (final DepositCollection pDeposit, final ServiceDocument pServiceDocument) throws SWORDException {
    try {
        ZipFileAccess tZipFile = new ZipFileAccess (super.getTempDir ());
        LOG.debug (""copying file"");
        String tZipTempFileName = super.getTempDir () + ""uploaded-file.tmp"";
        IOUtils.copy (pDeposit.getFile (), new FileOutputStream (tZipTempFileName));
        Datastream tDatastream = new LocalDatastream (super.getGenericFileName (pDeposit), this.getContentType (), tZipTempFileName);
        _datastreamList.add (tDatastream);
        _datastreamList.addAll (tZipFile.getFiles (tZipTempFileName));
        int i = 0;
        boolean found = false;
        for (i = 0; i < _datastreamList.size (); i ++) {
            if (_datastreamList.get (i).getId ().equalsIgnoreCase (""mets"")) {
                found = true;
                break;
            }
        }
        if (found) {
            SAXBuilder tBuilder = new SAXBuilder ();
            _mets = new METSObject (tBuilder.build (((LocalDatastream) _datastreamList.get (i)).getPath ()));
            LocalDatastream tLocalMETSDS = (LocalDatastream) _datastreamList.remove (i);
            new File (tLocalMETSDS.getPath ()).delete ();
            _datastreamList.add (_mets.getMETSDs ());
            _datastreamList.addAll (_mets.getMetadataDatastreams ());
        } else {
            throw new SWORDException (""Couldn't find a METS document in the zip file, ensure it is named mets.xml or METS.xml"");
        }
        SWORDEntry tEntry = super.ingestDepost (pDeposit, pServiceDocument);
        tZipFile.removeLocalFiles ();
        return tEntry;
    } catch (IOException tIOExcpt) {
        String tMessage = ""Couldn't retrieve METS from deposit: "" + tIOExcpt.toString ();
        LOG.error (tMessage);
        tIOExcpt.printStackTrace ();
        throw new SWORDException (tMessage, tIOExcpt);
    } catch (JDOMException tJDOMExcpt) {
        String tMessage = ""Couldn't build METS from deposit: "" + tJDOMExcpt.toString ();
        LOG.error (tMessage);
        tJDOMExcpt.printStackTrace ();
        throw new SWORDException (tMessage, tJDOMExcpt);
    }
}
",19687456,"public void testReadPerMemberSixSmall () throws IOException {
    GZIPMembersInputStream gzin = new GZIPMembersInputStream (new ByteArrayInputStream (sixsmall_gz));
    gzin.setEofEachMember (true);
    for (int i = 0;
    i < 3; i ++) {
        int count2 = IOUtils.copy (gzin, new NullOutputStream ());
        assertEquals (""wrong 1-byte member count"", 1, count2);
        gzin.nextMember ();
        int count3 = IOUtils.copy (gzin, new NullOutputStream ());
        assertEquals (""wrong 5-byte member count"", 5, count3);
        gzin.nextMember ();
    }
    int countEnd = IOUtils.copy (gzin, new NullOutputStream ());
    assertEquals (""wrong eof count"", 0, countEnd);
}
",Copy File,Type-3 (WT3/4),TRUE
1579007,"private void nextZipEntry (String url, int level) throws IOException {
    if (! url.startsWith (""META-INF/"") && ! url.startsWith (""OEBPS/"")) url = ""OEBPS/"" + url;

    ZipEntry ze = new ZipEntry (url);
    ze.setMethod (ZipEntry.DEFLATED);
    tmpzos.putNextEntry (ze);
}
",10178914,"private void writeEntry (File file, ZipOutputStream output, File oya) throws IOException {
    BufferedInputStream input = new BufferedInputStream (new FileInputStream (file));
    String fn = extractRelativeZipPath (file.getAbsolutePath (), oya.getAbsolutePath ());
    ZipEntry entry = new ZipEntry (this.convertZipEntrySeparator (fn));
    output.putNextEntry (entry);
    int b;
    while ((b = input.read ()) != - 1) {
        output.write (b);
    }
    input.close ();
    output.closeEntry ();
}
",Zip Files,Type-3 (WT3/4),FALSE
792644,"private static void readAndRewrite (File inFile, File outFile) throws IOException {
    ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile)));
    DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis);
    Dataset ds = DcmObjectFactory.getInstance ().newDataset ();
    dcmParser.setDcmHandler (ds.getDcmHandler ());
    dcmParser.parseDcmFile (null, Tags.PixelData);
    PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    System.out.println (""reading "" + inFile + ""..."");
    pdReader.readPixelData (false);
    ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile)));
    DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE;
    ds.writeDataset (out, dcmEncParam);
    ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ());
    System.out.println (""writing "" + outFile + ""..."");
    PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    pdWriter.writePixelData ();
    out.flush ();
    out.close ();
    System.out.println (""done!"");
}
",7119938,"public void putFile (CompoundName file, FileInputStream fileInput) throws IOException {
    File fullDir = new File (REMOTE_BASE_DIR.getCanonicalPath ());
    for (int i = 0;
    i < file.size () - 1; i ++) fullDir = new File (fullDir, file.get (i));

    fullDir.mkdirs ();
    File outputFile = new File (fullDir, file.get (file.size () - 1));
    FileOutputStream outStream = new FileOutputStream (outputFile);
    for (int byteIn = fileInput.read ();
    byteIn != - 1; byteIn = fileInput.read ()) outStream.write (byteIn);

    fileInput.close ();
    outStream.close ();
}
",Copy File,Type-3 (WT3/4),TRUE
4200038,"public static int getCrc32asInt (byte [] in) {
    if (in == null || in.length == 0) return - 1;

    CRC32 crc = new CRC32 ();
    crc.update (in);
    return (int) crc.getValue ();
}
",11911260,"private void readHeader () throws IOException {
    CRC32 headCRC = new CRC32 ();
    int magic = in.read ();
    if (magic < 0) {
        eos = true;
        return;
    }
    headCRC.update (magic);
    if (magic != (GZIP_MAGIC>> 8)) throw new IOException (""Error in GZIP header, first byte doesn't match"");

    magic = in.read ();
    if (magic != (GZIP_MAGIC & 0xff)) throw new IOException (""Error in GZIP header, second byte doesn't match"");

    headCRC.update (magic);
    int CM = in.read ();
    if (CM != 8) throw new IOException (""Error in GZIP header, data not in deflate format"");

    headCRC.update (CM);
    int flags = in.read ();
    if (flags < 0) throw new EOFException (""Early EOF in GZIP header"");

    headCRC.update (flags);
    if ((flags & 0xd0) != 0) throw new IOException (""Reserved flag bits in GZIP header != 0"");

    for (int i = 0;
    i < 6; i ++) {
        int readByte = in.read ();
        if (readByte < 0) throw new EOFException (""Early EOF in GZIP header"");

        headCRC.update (readByte);
    }
    if ((flags & FEXTRA) != 0) {
        for (int i = 0;
        i < 2; i ++) {
            int readByte = in.read ();
            if (readByte < 0) throw new EOFException (""Early EOF in GZIP header"");

            headCRC.update (readByte);
        }
        if (in.read () < 0 || in.read () < 0) throw new EOFException (""Early EOF in GZIP header"");

        int len1, len2, extraLen;
        len1 = in.read ();
        len2 = in.read ();
        if ((len1 < 0) || (len2 < 0)) throw new EOFException (""Early EOF in GZIP header"");

        headCRC.update (len1);
        headCRC.update (len2);
        extraLen = (len1 << 8) | len2;
        for (int i = 0;
        i < extraLen; i ++) {
            int readByte = in.read ();
            if (readByte < 0) throw new EOFException (""Early EOF in GZIP header"");

            headCRC.update (readByte);
        }
    }
    if ((flags & FNAME) != 0) {
        int readByte;
        while ((readByte = in.read ()) > 0) headCRC.update (readByte);

        if (readByte < 0) throw new EOFException (""Early EOF in GZIP file name"");

        headCRC.update (readByte);
    }
    if ((flags & FCOMMENT) != 0) {
        int readByte;
        while ((readByte = in.read ()) > 0) headCRC.update (readByte);

        if (readByte < 0) throw new EOFException (""Early EOF in GZIP comment"");

        headCRC.update (readByte);
    }
    if ((flags & FHCRC) != 0) {
        int tempByte;
        int crcval = in.read ();
        if (crcval < 0) throw new EOFException (""Early EOF in GZIP header"");

        tempByte = in.read ();
        if (tempByte < 0) throw new EOFException (""Early EOF in GZIP header"");

        crcval = (crcval << 8) | tempByte;
        if (crcval != ((int) headCRC.getValue () & 0xffff)) throw new IOException (""Header CRC value mismatch"");

    }
    readGZIPHeader = true;
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
1951108,"private void zipStream (InputStream inStream, String streamName, File zipFile) throws IOException {
    if (inStream == null) {
        log.warn (""No stream to zip."");
    } else {
        try {
            FileOutputStream dest = new FileOutputStream (zipFile);
            ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest));
            ZipEntry entry = new ZipEntry (streamName);
            out.putNextEntry (entry);
            copyInputStream (inStream, out);
            out.close ();
            dest.close ();
            inStream.close ();
        } catch (IOException e) {
            log.error (""IOException while zipping stream"");
            throw e;
        }
    }
}
",15891912,"public void close () {
    logger.debug (""Closing output file."");
    outfile.close ();
    tempFile.renameTo (new File (fileName));
    if (toZIP) {
        logger.debug (""ZIPping output file."");
        try {
            ZipOutputStream zipout = new ZipOutputStream (new FileOutputStream (fileName + "".zip""));
            zipout.setLevel (9);
            String outfilezipname = fileName.substring (fileName.lastIndexOf (System.getProperty (""file.separator"")) + 1);
            zipout.putNextEntry (new ZipEntry (outfilezipname));
            FileInputStream fis = new FileInputStream (fileName);
            byte [] buffer = new byte [65536];
            int len;
            while ((len = fis.read (buffer)) > 0) {
                zipout.write (buffer, 0, len);
            }
            zipout.close ();
            fis.close ();
            logger.debug (""ZIPping output file ok."");
            logger.debug (""Removing "" + fileName);
            (new File (fileName)).delete ();
        } catch (IOException ex) {
            logger.debug (""Error when zipping file"", ex);
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
1751009,"@BeforeClass
public static void createProblem () throws IOException, ParserConfigurationException, TransformerException {
    problem = File.createTempFile (""___prb___"", "".problem"");
    System.out.println (""created temporary problem "" + problem);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (problem));
    PrintStream ps = new PrintStream (zos);
    zos.putNextEntry (new ZipEntry (""MANIFEST""));
    DocumentBuilderFactory builderFactory = DocumentBuilderFactory.newInstance ();
    DocumentBuilder builder = builderFactory.newDocumentBuilder ();
    Document doc = builder.newDocument ();
    Element root = doc.createElement (""resources"");
    doc.appendChild (root);
    Element alias = doc.createElement (""alias"");
    alias.setAttribute (""path"", ""STATEMENT"");
    alias.setAttribute (""target"", ""statement.txt"");
    root.appendChild (alias);
    Element contents1 = doc.createElement (""contents"");
    contents1.setAttribute (""path"", ""ANSWER"");
    contents1.setTextContent (""42"");
    root.appendChild (contents1);
    Element contents2 = doc.createElement (""contents"");
    contents2.setAttribute (""path"", ""STATEMENT EXT"");
    contents2.setTextContent (""TXT"");
    root.appendChild (contents2);
    Element teacher = doc.createElement (""teacher"");
    teacher.setAttribute (""path"", ""ANSWER"");
    root.appendChild (teacher);
    Source source = new DOMSource (doc);
    Result result = new StreamResult (zos);
    Transformer xformer = TransformerFactory.newInstance ().newTransformer ();
    xformer.transform (source, result);
    zos.putNextEntry (new ZipEntry (""statement.txt""));
    ps.println (""���� ����� ������������ ����� � ����?"");
    zos.closeEntry ();
    zos.close ();
}
",13994366,"public static boolean exportStandalone (String projectDirectory, String destinyJARPath) {
    boolean exported = true;
    try {
        File destinyJarFile = new File (destinyJARPath);
        FileOutputStream mergedFile = new FileOutputStream (destinyJarFile);
        ZipOutputStream os = new ZipOutputStream (mergedFile);
        String manifest = Writer.defaultManifestFile (""es.eucm.eadventure.engine.EAdventureStandalone"");
        ZipEntry manifestEntry = new ZipEntry (""META-INF/MANIFEST.MF"");
        os.putNextEntry (manifestEntry);
        os.write (manifest.getBytes ());
        os.closeEntry ();
        os.flush ();
        File.mergeZipAndDirToJar (""web/eAdventure_temp.jar"", projectDirectory, os);
        addNeededLibrariesToJar (os, Controller.getInstance ());
        os.close ();
    } catch (FileNotFoundException e) {
        exported = false;
        ReportDialog.GenerateErrorReport (e, true, ""UNKNOWNERROR"");
    } catch (IOException e) {
        exported = false;
        ReportDialog.GenerateErrorReport (e, true, ""UNKNOWNERROR"");
    }
    return exported;
}
",Zip Files,Type-3 (WT3/4),FALSE
10407191,"@Override
public boolean copy (Document document, Folder folder) throws Exception {
    boolean isCopied = false;
    if (document.getId () != null && folder.getId () != null) {
        Document copiedDoc = new DocumentModel ();
        copiedDoc.setValues (document.getValues ());
        copiedDoc.setFolder (folder);
        copiedDoc.setId (null);
        em.persist (copiedDoc);
        resourceAuthorityService.applyAuthority (copiedDoc);
        List < Preference > preferences = prefService.findAll ();
        Preference preference = new PreferenceModel ();
        if (preferences != null && ! preferences.isEmpty ()) {
            preference = preferences.get (0);
        }
        String repo = preference.getRepository ();
        SimpleDateFormat sdf = new SimpleDateFormat (Constants.DATEFORMAT_YYYYMMDD);
        Calendar calendar = Calendar.getInstance ();
        StringBuffer sbRepo = new StringBuffer (repo);
        sbRepo.append (File.separator);
        StringBuffer sbFolder = new StringBuffer (sdf.format (calendar.getTime ()));
        sbFolder.append (File.separator).append (calendar.get (Calendar.HOUR_OF_DAY));
        File fFolder = new File (sbRepo.append (sbFolder).toString ());
        if (! fFolder.exists ()) {
            fFolder.mkdirs ();
        }
        copiedDoc.setLocation (sbFolder.toString ());
        em.merge (copiedDoc);
        File in = new File (repo + File.separator + document.getLocation () + File.separator + document.getId () + ""."" + document.getExt ());
        File out = new File (fFolder.getAbsolutePath () + File.separator + copiedDoc.getId () + ""."" + copiedDoc.getExt ());
        FileChannel inChannel = new FileInputStream (in).getChannel ();
        FileChannel outChannel = new FileOutputStream (out).getChannel ();
        try {
            inChannel.transferTo (0, inChannel.size (), outChannel);
        } catch (IOException e) {
            throw e;
        } finally {
            if (inChannel != null) inChannel.close ();

            if (outChannel != null) outChannel.close ();

        }
    }
    return isCopied;
}
",18583832,"private static void copy (File source, File target) throws IOException {
    FileInputStream from = null;
    FileOutputStream to = null;
    try {
        from = new FileInputStream (source);
        to = new FileOutputStream (target);
        byte [] buffer = new byte [4096];
        int bytesRead;
        while ((bytesRead = from.read (buffer)) != - 1) to.write (buffer, 0, bytesRead);

    } finally {
        if (from != null) try {
            from.close ();
        } catch (IOException e) {
        }

        if (to != null) try {
            to.close ();
        } catch (IOException e) {
        }

    }
}
",Copy File,Type-3 (WT3/4),TRUE
251963,"File createJar (File jar, String...entries) throws IOException {
    OutputStream out = new FileOutputStream (jar);
    try {
        JarOutputStream jos = new JarOutputStream (out);
        for (String e : entries) {
            jos.putNextEntry (new JarEntry (getPathForZipEntry (e)));
            jos.write (getBodyForEntry (e).getBytes ());
        }
        jos.close ();
    } finally {
        out.close ();
    }
    return jar;
}
",23188868,"public void run (IProgressMonitor runnerMonitor) throws CoreException {
    try {
        Map < String, File > projectFiles = new HashMap < String, File > ();
        IPath basePath = new Path (""/"");
        for (File nextLocation : filesToZip) {
            projectFiles.putAll (getFilesToZip (nextLocation, basePath, fileFilter));
        }
        if (projectFiles.isEmpty ()) {
            PlatformActivator.logDebug (""Zip file ("" + zipFileName + "") not created because there were no files to zip"");
            return;
        }
        IPath resultsPath = PlatformActivator.getDefault ().getResultsPath ();
        File copyRoot = resultsPath.toFile ();
        copyRoot.mkdirs ();
        IPath zipFilePath = resultsPath.append (new Path (finalZip));
        String zipFileName = zipFilePath.toPortableString ();
        ZipOutputStream out = new ZipOutputStream (new FileOutputStream (zipFileName));
        try {
            out.setLevel (Deflater.DEFAULT_COMPRESSION);
            for (String filePath : projectFiles.keySet ()) {
                File nextFile = projectFiles.get (filePath);
                FileInputStream fin = new FileInputStream (nextFile);
                try {
                    out.putNextEntry (new ZipEntry (filePath));
                    try {
                        byte [] bin = new byte [4096];
                        int bread = fin.read (bin, 0, 4096);
                        while (bread != - 1) {
                            out.write (bin, 0, bread);
                            bread = fin.read (bin, 0, 4096);
                        }
                    } finally {
                        out.closeEntry ();
                    }
                } finally {
                    fin.close ();
                }
            }
        } finally {
            out.close ();
        }
    } catch (FileNotFoundException e) {
        Status error = new Status (Status.ERROR, PlatformActivator.PLUGIN_ID, Status.ERROR, e.getLocalizedMessage (), e);
        throw new CoreException (error);
    } catch (IOException e) {
        Status error = new Status (Status.ERROR, PlatformActivator.PLUGIN_ID, Status.ERROR, e.getLocalizedMessage (), e);
        throw new CoreException (error);
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
3230278,"public static long getCRC (String content) {
    if (content.length () == 0) return 0;

    final java.util.zip.CRC32 crc = new java.util.zip.CRC32 ();
    java.io.OutputStream crcOut = new java.io.OutputStream () {
        @Override
        public void write (int b) throws java.io.IOException {
            crc.update (b);
        }}

    ;
    try {
        new java.io.OutputStreamWriter (crcOut).write (content);
    } catch (java.io.IOException e) {
        throw new IllegalStateException (""Could not check CRC of message"");
    }
    return crc.getValue ();
}
",23677203,"public static long checksum1 (File file) throws IOException {
    CRC32 crc = new CRC32 ();
    FileReader fr = new FileReader (file);
    int data;
    while ((data = fr.read ()) != - 1) {
        crc.update (data);
    }
    fr.close ();
    return crc.getValue ();
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
160739,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",18875576,"public static < T extends ZipNode > void saveAll (OutputStream outputstream, Collection < T > list, ZipStreamFilter filter) throws Exception {
    ZipOutputStream zip_out = new ZipOutputStream (outputstream);
    try {
        ZipEntry entry = new ZipEntry ("".info/info.properties"");
        entry.setTime (0);
        zip_out.putNextEntry (entry);
        String info = ""filter = "" + filter.getClass ().getName () + ""\n"" + ""count  = "" + list.size () + ""\n"";
        zip_out.write (info.getBytes ());
        for (T object : list) {
            save (zip_out, object, filter);
        }
    } catch (Throwable ex) {
        ex.printStackTrace ();
    } finally {
        try {
            zip_out.close ();
        } catch (IOException e) {
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
1936137,"public void preparaEscrita (DadosSeriais dados, String dir) throws BasicException {
    String idArquivo = dados.getIdColeta ().toString ();
    if (dados.getIdResumo () != null) {
        idArquivo += ""_"" + dados.getIdResumo ().toString ();
    }
    if (dir == null || dir.trim ().equals ("""")) {
        throw BasicException.errorHandling (""Diret�rio Imagem de Dados n�o foi definido."", ""msgErroNaoExisteDiretorioImagem"", new String [] {}, log);
    }
    try {
        fos = new FileOutputStream (new File (dir.trim (), ""pdump."" + idArquivo + "".data.xml.zip""));
    } catch (FileNotFoundException e) {
        throw BasicException.errorHandling (""Erro ao abrir arquivo de dados xml para escrita"", ""msgErroCriarArquivoDadosXML"", e, log);
    }
    zipOutputStream = new ZipOutputStream (fos);
    zipOutputStream.setLevel (Deflater.DEFAULT_COMPRESSION);
    try {
        zipOutputStream.putNextEntry (new ZipEntry (""pdump."" + idArquivo + "".data.xml""));
        xmlWriter = XMLOutputFactory.newInstance ().createXMLStreamWriter (zipOutputStream, ENCODING);
    } catch (Exception e) {
        throw BasicException.errorHandling (""Erro ao criar entrada em arquivo compactado"", ""msgErroCriarEntradaZipArquivoDadosXML"", e, log);
    }
    XMLStreamWriter osw = null;
    try {
        xmlWriter = XMLOutputFactory.newInstance ().createXMLStreamWriter (zipOutputStream, ENCODING);
    } catch (Exception e) {
        throw BasicException.errorHandling (""Erro ao criar entrada em arquivo compactado"", ""msgErroCriarEntradaZipArquivoDadosXML"", e, log);
    }
    SimpleDateFormat dateFormat = new SimpleDateFormat (""yyyy-MM-dd'T'HH:mm:ss"");
    if (dados.getTipos ().size () > 0) {
        tipos = new int [dados.getTipos ().size ()];
        for (int c = 0;
        c < dados.getTipos ().size (); c ++) {
            String tipo = dados.getTipos ().get (c);
            if (tipo.equals (LIT_INTEIRO)) {
                tipos [c] = INTEIRO;
            } else if (tipo.equals (LIT_DECIMAL)) {
                tipos [c] = DECIMAL;
            } else if (tipo.equals (LIT_DATA)) {
                tipos [c] = DATA;
            } else {
                tipos [c] = TEXTO;
            }

        }
    }
    try {
        xmlWriter.writeStartDocument (ENCODING, ""1.0"");
        xmlWriter.writeStartElement (""coleta"");
        xmlWriter.writeAttribute (""xmlns:xsi"", ""http://www.w3.org/2001/XMLSchema-instance"");
        xmlWriter.writeAttribute (""xsi:noNamespaceSchemaLocation"", ""http://www.pingifes.lcc.ufmg.br/dtd/pingifes_dados_seriais.xsd"");
        xmlWriter.writeStartElement (""id"");
        xmlWriter.writeCharacters (idArquivo);
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""data"");
        xmlWriter.writeCharacters (dateFormat.format (dados.getDataColeta ()));
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""sql"");
        xmlWriter.writeCData (dados.getSql ());
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""cabecalho"");
        for (int c = 0;
        c < dados.getCabecalho ().size (); c ++) {
            xmlWriter.writeStartElement (""nome"");
            xmlWriter.writeAttribute (""tipo"", dados.getTipos ().get (c));
            xmlWriter.writeCharacters (dados.getCabecalho ().get (c));
            xmlWriter.writeEndElement ();
        }
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""quantidade"");
        xmlWriter.writeCharacters ("""" + dados.getQuantidade ());
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""dados"");
    } catch (XMLStreamException e) {
        throw BasicException.errorHandling (""Erro ao escrever dados em arquivo compactado"", ""msgErroEscreverArquivoDadosXML"", e, log);
    }
    calculadorHash = new CalculaHash ();
}
",11514192,"private void zipDir (File dir, String jarEntry, JarOutputStream jos) throws IOException {
    String [] dirList = dir.list ();
    for (int i = 0;
    i < dirList.length; i ++) {
        File f = new File (dir, dirList [i]);
        if (f.isDirectory ()) {
            zipDir (f, jarEntry + dirList [i] + File.separatorChar, jos);
            continue;
        }
        FileInputStream fis = new FileInputStream (f);
        ZipEntry anEntry = new ZipEntry (jarEntry + dirList [i]);
        jos.putNextEntry (anEntry);
        byte [] readBuffer = new byte [2156];
        int bytesIn = 0;
        while ((bytesIn = fis.read (readBuffer)) != - 1) {
            jos.write (readBuffer, 0, bytesIn);
        }
        fis.close ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
1514106,"private void exportLearningUnitView (File selectedFile) {
    if (learningUnitViewElementsManager.isOriginalElementsOnly ()) {
        String [] elementIds = learningUnitViewElementsManager.getAllLearningUnitViewElementIds ();
        for (int i = 0;
        i < elementIds.length; i ++) {
            FSLLearningUnitViewElement element = learningUnitViewElementsManager.getLearningUnitViewElement (elementIds [i], false);
            if (element.getLastModificationDate () == null) {
                element.setLastModificationDate (String.valueOf (new Date ().getTime ()));
                element.setModified (true);
            }
        }
        learningUnitViewElementsManager.setModified (true);
        learningUnitViewManager.saveLearningUnitViewData ();
        if (selectedFile != null) {
            try {
                File outputFile = selectedFile;
                String fileName = outputFile.getName ();
                StringBuffer extension = new StringBuffer ();
                if (fileName.length () >= 5) {
                    for (int i = 5;
                    i > 0; i --) {
                        extension.append (fileName.charAt (fileName.length () - i));
                    }
                }
                if (! extension.toString ().equals ("".fslv"")) {
                    outputFile.renameTo (new File (outputFile.getAbsolutePath () + "".fslv""));
                    outputFile = new File (outputFile.getAbsolutePath () + "".fslv"");
                }
                File files [] = selectedFile.getParentFile ().listFiles ();
                int returnValue = FLGOptionPane.OK_OPTION;
                for (int i = 0;
                i < files.length; i ++) {
                    if (outputFile.getAbsolutePath ().equals (files [i].getAbsolutePath ())) {
                        returnValue = FLGOptionPane.showConfirmDialog (internationalization.getString (""dialog.exportLearningUnitView.fileExits.message""), internationalization.getString (""dialog.exportLearningUnitView.fileExits.title""), FLGOptionPane.OK_CANCEL_OPTION, FLGOptionPane.QUESTION_MESSAGE);
                        break;
                    }
                }
                if (returnValue == FLGOptionPane.OK_OPTION) {
                    FileOutputStream os = new FileOutputStream (outputFile);
                    ZipOutputStream zipOutputStream = new ZipOutputStream (os);
                    ZipEntry zipEntry = new ZipEntry (""dummy"");
                    zipOutputStream.putNextEntry (zipEntry);
                    zipOutputStream.closeEntry ();
                    zipOutputStream.flush ();
                    zipOutputStream.finish ();
                    zipOutputStream.close ();
                    final File outFile = outputFile;
                    (new Thread () {
                        public void run () {
                            try {
                                ZipOutputStream zipOutputStream = new ZipOutputStream (new FileOutputStream (outFile));
                                File [] files = (new File (learningUnitViewManager.getLearningUnitViewOriginalDataDirectory ().getPath ())).listFiles ();
                                int maxSteps = files.length;
                                int step = 1;
                                exportProgressDialog = new FLGImageProgressDialog (null, 0, maxSteps, 0, getClass ().getClassLoader ().getResource (""freestyleLearning/homeCore/images/fsl.gif""), (Color) UIManager.get (""FSLColorBlue""), (Color) UIManager.get (""FSLColorRed""), internationalization.getString (""learningUnitViewExport.rogressbarText""));
                                exportProgressDialog.setCursor (new Cursor (Cursor.WAIT_CURSOR));
                                exportProgressDialog.setBarValue (step);
                                buildExportZipFile ("""", zipOutputStream, files, step);
                                zipOutputStream.flush ();
                                zipOutputStream.finish ();
                                zipOutputStream.close ();
                                exportProgressDialog.setBarValue (maxSteps);
                                exportProgressDialog.setCursor (new Cursor (Cursor.DEFAULT_CURSOR));
                                exportProgressDialog.dispose ();
                            } catch (Exception e) {
                                e.printStackTrace ();
                            }
                        }}

                    ).start ();
                    os.close ();
                }
            } catch (Exception exp) {
                exp.printStackTrace ();
            }
        }
    } else {
    }
}
",9161482,"public static void addToJar (JarOutputStream jos, JarFile jf) throws IOException {
    Enumeration e = jf.entries ();
    while (e.hasMoreElements ()) {
        ZipEntry je = (ZipEntry) e.nextElement ();
        InputStream io = jf.getInputStream (je);
        byte b [] = new byte [4096];
        int read = 0;
        try {
            jos.putNextEntry (je);
            while ((read = io.read (b, 0, 4096)) != - 1) {
                jos.write (b, 0, read);
            }
        } catch (ZipException ze) {
            throw ze;
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
2016059,"private void ZipCode (NpsContext ctxt, ZipOutputStream out) throws Exception {
    String filename = ""JOB"" + GetId () + "".data"";
    out.putNextEntry (new ZipEntry (filename));
    try {
        ZipWriter writer = new ZipWriter (out);
        writer.print (code);
    } finally {
        out.closeEntry ();
    }
}
",8703701,"private byte [] injectModifiedText () {
    byte [] buffer = new byte [BUFFER_SIZE];
    boolean contentFound = false;
    boolean stylesFound = false;
    ByteArrayOutputStream out = new ByteArrayOutputStream (2 * fileData.length);
    ZipOutputStream zipOutputStream = new ZipOutputStream (out);
    ZipInputStream zipInputStream = new ZipInputStream (new ByteArrayInputStream (fileData));
    try {
        ZipEntry zipEntry = zipInputStream.getNextEntry ();
        while (zipEntry != null) {
            zipOutputStream.putNextEntry (new ZipEntry (zipEntry.getName ()));
            if (content != null && zipEntry.getName ().equals (""content.xml"")) {
                contentFound = true;
                if (log.isTraceEnabled ()) {
                    log.trace (""Write content.xml to fileData\n"" + content);
                } else if (log.isDebugEnabled ()) {
                    log.trace (""Write content.xml to fileData, length = "" + content.length ());
                }

                zipOutputStream.write (content.getBytes (""UTF-8""));
            } else if (styles != null && zipEntry.getName ().equals (""styles.xml"")) {
                stylesFound = true;
                if (log.isTraceEnabled ()) {
                    log.trace (""Write styles.xml to fileData\n"" + styles);
                } else if (log.isDebugEnabled ()) {
                    log.debug (""Write styles.xml to fileData, length = "" + styles.length ());
                }

                zipOutputStream.write (styles.getBytes (""UTF-8""));
            } else {
                int read = zipInputStream.read (buffer);
                while (read > - 1) {
                    zipOutputStream.write (buffer, 0, read);
                    read = zipInputStream.read (buffer);
                }
            }

            zipEntry = zipInputStream.getNextEntry ();
        }
    } catch (IOException ex) {
        log.error (""Exception while injecting content and styles into odt"", ex);
        throw new IllegalArgumentException (""fileData is probably not an odt file: "" + ex);
    } finally {
        IOUtils.closeQuietly (zipInputStream);
        IOUtils.closeQuietly (zipOutputStream);
    }
    if (content != null && ! contentFound) {
        log.error (""fileData is not an odt file, no content.xml found, throwing exception."");
        throw new IllegalArgumentException (""fileData is not an odt file, no content.xml found"");
    }
    if (styles != null && ! stylesFound) {
        log.error (""fileData is not an odt file, no styles.xml found, throwing exception."");
        throw new IllegalArgumentException (""fileData is not an odt file, no styles.xml found"");
    }
    byte [] result = out.toByteArray ();
    if (log.isDebugEnabled ()) {
        log.debug (""Injected content. File data changed from "" + fileData.length + "" bytes to "" + result.length + "" bytes."");
    }
    return result;
}
",Zip Files,Type-3 (WT3/4),FALSE
1446727,"private void backupDiskFile (ZipOutputStream out, String fileName, DiskFile file) throws SQLException, IOException {
    Database db = session.getDatabase ();
    fileName = FileUtils.getFileName (fileName);
    out.putNextEntry (new ZipEntry (fileName));
    int pos = - 1;
    int max = file.getReadCount ();
    while (true) {
        pos = file.copyDirect (pos, out);
        if (pos < 0) {
            break;
        }
        db.setProgress (DatabaseEventListener.STATE_BACKUP_FILE, fileName, pos, max);
    }
    out.closeEntry ();
}
",18195007,"private void zipFiles () throws ZipException, IOException {
    ZipOutputStream zipOuputStream = new ZipOutputStream (new FileOutputStream (zipFile));
    for (File sourceDir : sourceDirs) {
        File [] sourceFiles = sourceDir.listFiles (new SourceFileFilter ());
        if (sourceFiles != null) {
            for (File sourceFile : sourceFiles) {
                ZipEntry zipEntry = new ZipEntry (sourceFile.getName ());
                zipOuputStream.putNextEntry (zipEntry);
                if (logger.isInfoEnabled ()) {
                    logger.info (""Adding zip entry "" + sourceFile.getAbsolutePath () + "" to "" + zipFile.getAbsolutePath ());
                }
                if (sourceFile.length () > BYTE_ARRAY_BUFF_SIZE) {
                    BufferedInputStream bis = new BufferedInputStream (new FileInputStream (sourceFile), BYTE_ARRAY_BUFF_SIZE);
                    byte [] buf = new byte [BYTE_ARRAY_BUFF_SIZE];
                    int b;
                    while ((b = bis.read (buf, 0, BYTE_ARRAY_BUFF_SIZE)) != - 1) {
                        zipOuputStream.write (buf, 0, b);
                    }
                    bis.close ();
                } else {
                    byte [] fileContents = FileUtil.getFileContentsAsByteArray (sourceFile);
                    zipOuputStream.write (fileContents);
                }
                zipOuputStream.closeEntry ();
            }
        }
    }
    zipOuputStream.close ();
}
",Zip Files,Type-3 (WT3/4),FALSE
2096403,"static void writeZipEntry (final byte [] data, final ZipOutputStream out, final ZipEntry entry, final boolean isCopy) throws IOException {
    if (isCopy) {
        out.putNextEntry (entry);
        try {
            out.write (data);
        } finally {
            out.closeEntry ();
        }
    } else {
        final ZipEntry entryCopy = new ZipEntry (entry.getName ());
        entryCopy.setTime (entry.getTime ());
        entryCopy.setMethod (ZipOutputStream.STORED);
        entryCopy.setSize (data.length);
        entryCopy.setCompressedSize (data.length);
        final CRC32 crc = new CRC32 ();
        crc.update (data);
        entryCopy.setCrc (crc.getValue ());
        out.putNextEntry (entryCopy);
        try {
            out.write (data);
        } finally {
            out.closeEntry ();
        }
    }
}
",6650088,"public int calculateCRC () {
    CRC32 crc = new CRC32 ();
    crc.reset ();
    crc.update (getData (), 2, getData ().length - 2);
    return (short) (crc.getValue ());
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
1177247,"@Override
public void write (DataOutput dataOutput, byte [] object) throws IOException {
    ZipOutputStream zos = new ZipOutputStream (new DataOutputOutputStream (dataOutput));
    zos.setMethod (ZipOutputStream.DEFLATED);
    zos.putNextEntry (new ZipEntry (""a""));
    zos.write (object, 0, object.length);
    zos.finish ();
    zos.close ();
}
",15468308,"private void archiveDirectory (ZipOutputStream out, File dir, String path) throws IOException {
    byte [] buf = new byte [16384];
    File [] files = dir.listFiles ();
    if (files.length > 0) {
        for (int x = 0;
        x < files.length; x ++) {
            if (files [x].isFile ()) {
                FileInputStream in = new FileInputStream (files [x]);
                out.putNextEntry (new ZipEntry (path + files [x].getName ()));
                int len;
                while ((len = in.read (buf)) > 0) {
                    out.write (buf, 0, len);
                }
                out.closeEntry ();
                in.close ();
            } else {
                archiveDirectory (out, files [x], path + files [x].getName () + File.separator);
            }
        }
    } else {
        out.putNextEntry (new ZipEntry (path));
        out.closeEntry ();
    }
}
",Zip Files,Type-3 (WT3/4),TRUE
2016059,"private void ZipCode (NpsContext ctxt, ZipOutputStream out) throws Exception {
    String filename = ""JOB"" + GetId () + "".data"";
    out.putNextEntry (new ZipEntry (filename));
    try {
        ZipWriter writer = new ZipWriter (out);
        writer.print (code);
    } finally {
        out.closeEntry ();
    }
}
",3720682,"@Override
protected void doGet (HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException {
    ZipOutputStream zipout = new ZipOutputStream (resp.getOutputStream ());
    ZipOutputStream zipout2 = new ZipOutputStream (new FileOutputStream (new File (""c:/t.zip"")));
    for (int i = 0;
    i < 200; i ++) {
        BufferedImage img = new BufferedImage (800 + i, 600 + i, BufferedImage.TYPE_INT_RGB);
        Graphics2D g = (Graphics2D) img.getGraphics ();
        g.setPaint (new GradientPaint (0, 0, Color.YELLOW, img.getWidth () - 1, img.getHeight () - 1, Color.BLUE, true));
        g.fillRect (0, 0, img.getWidth (), img.getHeight ());
        for (int t = 0;
        t < img.getHeight (); t += 10) {
            g.setColor (new Color (t + 1 * 100 + 1 * 10000));
            g.drawLine (0, t, img.getWidth (), t);
        }
        g.dispose ();
        ZipEntry entry = new ZipEntry (""hoge"" + i + "".bmp"");
        zipout.putNextEntry (entry);
        ImageIO.write (img, ""bmp"", zipout);
        ZipEntry entry2 = new ZipEntry (""hoge"" + i + "".bmp"");
        zipout2.putNextEntry (entry2);
        ImageIO.write (img, ""bmp"", zipout2);
    }
    zipout.close ();
    zipout2.close ();
}
",Zip Files,Type-3 (WT3/4),FALSE
6457199,"protected boolean doRequest (HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
    String path = request.getPathInfo ();
    if (! path.startsWith (alias)) {
        throw new ServletException (""Path '"" + path + ""' does not start with registered alias '"" + alias + ""'"");
    }
    String internal;
    if (alias.equals (""/"")) {
        internal = name + path;
    } else {
        internal = name + path.substring (alias.length (), path.length ());
    }
    URL resource = httpContext.getResource (internal);
    if (resource == null) {
        return false;
    }
    String mimeType = servletContext.getMimeType (internal);
    if (mimeType != null) {
        response.setContentType (mimeType);
    }
    InputStream is = resource.openStream ();
    OutputStream os = response.getOutputStream ();
    IOUtils.copyAndClose (is, os);
    return true;
}
",16227459,"public CmsSetupTestResult execute (CmsSetupBean setupBean) {
    CmsSetupTestResult testResult = new CmsSetupTestResult (this);
    String basePath = setupBean.getWebAppRfsPath ();
    if (! basePath.endsWith (File.separator)) {
        basePath += File.separator;
    }
    File file1;
    Random rnd = new Random ();
    do {
        file1 = new File (basePath + ""test"" + rnd.nextInt (1000));
    } while (file1.exists ());
    boolean success = false;
    try {
        file1.createNewFile ();
        FileWriter fw = new FileWriter (file1);
        fw.write (""aA1"");
        fw.close ();
        success = true;
        FileReader fr = new FileReader (file1);
        success = success && (fr.read () == 'a');
        success = success && (fr.read () == 'A');
        success = success && (fr.read () == '1');
        success = success && (fr.read () == - 1);
        fr.close ();
        success = file1.delete ();
        success = ! file1.exists ();
    } catch (Exception e) {
        success = false;
    }
    if (! success) {
        testResult.setRed ();
        testResult.setInfo (""OpenCms cannot be installed without read and write privileges for path "" + basePath + ""! Please check you are running your servlet container with the right user and privileges."");
        testResult.setHelp (""Not enough permissions to create/read/write a file"");
        testResult.setResult (RESULT_FAILED);
    } else {
        testResult.setGreen ();
        testResult.setResult (RESULT_PASSED);
    }
    return testResult;
}
",Copy File,Type-3 (WT3/4),TRUE
1446726,"private void backupPageStore (ZipOutputStream out, String fileName, PageStore store) throws SQLException, IOException {
    Database db = session.getDatabase ();
    fileName = FileUtils.getFileName (fileName);
    out.putNextEntry (new ZipEntry (fileName));
    int max = store.getPageCount ();
    int pos = 0;
    while (true) {
        pos = store.copyDirect (pos, out);
        if (pos < 0) {
            break;
        }
        db.setProgress (DatabaseEventListener.STATE_BACKUP_FILE, fileName, pos, max);
    }
    out.closeEntry ();
}
",23421923,"void writeRawDataFile (RawDataFileImpl rawDataFile, int number) throws IOException, TransformerConfigurationException, SAXException {
    numOfScans = rawDataFile.getNumOfScans ();
    dataPointsOffsets = rawDataFile.getDataPointsOffsets ();
    dataPointsLengths = rawDataFile.getDataPointsLengths ();
    consolidatedDataPointsOffsets = new TreeMap < Integer, Long > ();
    logger.info (""Saving data points of: "" + rawDataFile.getName ());
    String rawDataSavedName = ""Raw data file #"" + number + "" "" + rawDataFile.getName ();
    zipOutputStream.putNextEntry (new ZipEntry (rawDataSavedName + "".scans""));
    long newOffset = 0;
    byte buffer [] = new byte [1 << 20];
    RandomAccessFile dataPointsFile = rawDataFile.getDataPointsFile ();
    for (Integer storageID : dataPointsOffsets.keySet ()) {
        if (canceled) return;

        final long offset = dataPointsOffsets.get (storageID);
        dataPointsFile.seek (offset);
        final int bytes = dataPointsLengths.get (storageID) * 4 * 2;
        consolidatedDataPointsOffsets.put (storageID, newOffset);
        if (buffer.length < bytes) {
            buffer = new byte [bytes * 2];
        }
        dataPointsFile.read (buffer, 0, bytes);
        zipOutputStream.write (buffer, 0, bytes);
        newOffset += bytes;
        progress = 0.9 * ((double) offset / dataPointsFile.length ());
    }
    if (canceled) return;

    logger.info (""Saving raw data description of: "" + rawDataFile.getName ());
    zipOutputStream.putNextEntry (new ZipEntry (rawDataSavedName + "".xml""));
    OutputStream finalStream = zipOutputStream;
    StreamResult streamResult = new StreamResult (finalStream);
    SAXTransformerFactory tf = (SAXTransformerFactory) SAXTransformerFactory.newInstance ();
    TransformerHandler hd = tf.newTransformerHandler ();
    Transformer serializer = hd.getTransformer ();
    serializer.setOutputProperty (OutputKeys.INDENT, ""yes"");
    serializer.setOutputProperty (OutputKeys.ENCODING, ""UTF-8"");
    hd.setResult (streamResult);
    hd.startDocument ();
    saveRawDataInformation (rawDataFile, hd);
    hd.endDocument ();
}
",Zip Files,Type-3 (WT3/4),FALSE
5271797,"private void loadMap () {
    final String wordList = ""vietwordlist.txt"";
    try {
        File dataFile = new File (supportDir, wordList);
        if (! dataFile.exists ()) {
            final ReadableByteChannel input = Channels.newChannel (ClassLoader.getSystemResourceAsStream (""dict/"" + dataFile.getName ()));
            final FileChannel output = new FileOutputStream (dataFile).getChannel ();
            output.transferFrom (input, 0, 1000000L);
            input.close ();
            output.close ();
        }
        long fileLastModified = dataFile.lastModified ();
        if (map == null) {
            map = new HashMap ();
        } else {
            if (fileLastModified <= mapLastModified) {
                return;
            }
            map.clear ();
        }
        mapLastModified = fileLastModified;
        BufferedReader bs = new BufferedReader (new InputStreamReader (new FileInputStream (dataFile), ""UTF-8""));
        String accented;
        while ((accented = bs.readLine ()) != null) {
            String plain = VietUtilities.stripDiacritics (accented);
            map.put (plain.toLowerCase (), accented);
        }
        bs.close ();
    } catch (IOException e) {
        map = null;
        e.printStackTrace ();
        JOptionPane.showMessageDialog (this, myResources.getString (""Cannot_find_\"""") + wordList + myResources.getString (""\""_in\n"") + supportDir.toString (), VietPad.APP_NAME, JOptionPane.ERROR_MESSAGE);
    }
}
",10478671,"private void copyFile (File sourcefile, File targetfile) {
    BufferedInputStream in = null;
    BufferedOutputStream out = null;
    try {
        in = new BufferedInputStream (new FileInputStream (sourcefile));
        out = new BufferedOutputStream (new FileOutputStream (targetfile));
        byte [] buffer = new byte [4096];
        int bytesread = 0;
        while ((bytesread = in.read (buffer)) >= 0) {
            out.write (buffer, 0, bytesread);
        }
    } catch (IOException e) {
        e.printStackTrace ();
    } finally {
        try {
            if (in != null) {
                in.close ();
            }
            if (out != null) {
                out.close ();
            }
        } catch (IOException e) {
            e.printStackTrace ();
        }
    }
}
",Copy File,Type-3 (WT3/4),TRUE
732800,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",5245205,"private void writeDynData (final int time_s) throws IOException {
    this.zos.putNextEntry (new ZipEntry (""step."" + time_s + "".bin""));
    this.outFile = new DataOutputStream (this.zos);
    this.buf.position (0);
    this.outFile.writeDouble (time_s);
    this.quad.writeDynData (null, this.buf);
    this.outFile.writeInt (this.buf.position ());
    this.outFile.write (this.buf.array (), 0, this.buf.position ());
    this.zos.closeEntry ();
}
",Zip Files,Type-3 (WT3/4),FALSE
1409148,"public static int save () {
    try {
        String filename = ""tyrant.sav"";
        FileDialog fd = new FileDialog (new Frame (), ""Save Game"", FileDialog.SAVE);
        fd.setFile (filename);
        fd.setVisible (true);
        if (fd.getFile () != null) {
            filename = fd.getDirectory () + fd.getFile ();
        } else {
            return 0;
        }
        FileOutputStream f = new FileOutputStream (filename);
        ZipOutputStream z = new ZipOutputStream (f);
        z.putNextEntry (new ZipEntry (""data.xml""));
        if (! save (new ObjectOutputStream (z))) {
            throw new Error (""Save game failed"");
        }
        Game.message (""Game saved - "" + filename);
        z.closeEntry ();
        z.close ();
        if (saveHasBeenCalledAlready) Game.message (""Please note that you can only restore the game with the same version of Tyrant (v"" + VERSION + "")."");

        saveHasBeenCalledAlready = false;
    } catch (Exception e) {
        Game.message (""Error while saving: "" + e.toString ());
        if (QuestApp.isapplet) {
            Game.message (""This may be due to your browser security restrictions"");
            Game.message (""If so, run the web start or downloaded application version instead"");
        }
        System.out.println (e);
        return - 1;
    }
    return 1;
}
",14203228,"private void writeEntry (byte [] data, String name, ZipOutputStream outStream) throws IOException {
    ZipEntry entry = new ZipEntry (name);
    entry.setSize (data.length);
    entry.setTime (System.currentTimeMillis ());
    if (outStream != null) {
        outStream.putNextEntry (entry);
        outStream.write (data);
        outStream.closeEntry ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
1287866,"private void cleanupStagingEnvironment (File stagingDir) throws FileUpdateException {
    if (stagingDir != null && stagingDir.exists () && stagingDir.isDirectory ()) {
        File [] files = stagingDir.listFiles ();
        for (int i = 0;
        i < files.length; i ++) {
            File f = files [i];
            if (! f.delete ()) {
                logger.error (""Could not delete: "" + f.getAbsolutePath ());
                throw new SessionEnvironmentException (""Could not delete: "" + f.getAbsolutePath ());
            }
        }
        if (stagingDir.exists ()) {
            if (stagingDir.delete ()) {
                logger.debug (stagingDir + "" was successfully deleted"");
            } else {
                logger.error (""Could not clean up staging directory: "" + stagingDir.getAbsolutePath ());
                throw new SessionEnvironmentException (""Could not remove directory: "" + stagingDir.getAbsolutePath ());
            }
        }
    } else {
        throw new SessionEnvironmentException (""Staging directory undefined, does not exist, or is not a directory"");
    }
}
",2641959,"public static boolean deleteDir (File dir) {
    if (dir.exists ()) {
        File [] files = dir.listFiles ();
        for (int i = 0;
        i < files.length; i ++) {
            if (files [i].isDirectory ()) {
                deleteDir (files [i]);
            } else {
                files [i].delete ();
            }
        }
    }
    return (dir.delete ());
}
",Delete Folder and Contents,Type-3 (WT3/4),FALSE
112054,"private void exportAllSettings (HTTPurl urlData, OutputStream outStream) throws Exception {
    CaptureDeviceList devList = CaptureDeviceList.getInstance ();
    if (devList.getActiveDeviceCount () > 0) {
        PageTemplate template = new PageTemplate (store.getProperty (""path.template"") + File.separator + ""SettingsLoad.html"");
        StringBuffer buff = new StringBuffer ();
        buff.append (""<tr><td><img border=0 src='/images/stop.png' align='absmiddle' width='24' height='24'></td><td>Can not save settings while a capture is in progress.</td></tr>"");
        template.replaceAll (""$result"", buff.toString ());
        outStream.write (template.getPageBytes ());
        return;
    }
    boolean matchList = ""true"".equalsIgnoreCase (urlData.getParameter (""MatchList""));
    boolean autoAdd = ""true"".equalsIgnoreCase (urlData.getParameter (""AutoAdd""));
    boolean channelMapping = ""true"".equalsIgnoreCase (urlData.getParameter (""ChannelMapping""));
    boolean deviceSelection = ""true"".equalsIgnoreCase (urlData.getParameter (""DeviceSelection""));
    boolean agentMapping = ""true"".equalsIgnoreCase (urlData.getParameter (""AgentMapping""));
    boolean channels = ""true"".equalsIgnoreCase (urlData.getParameter (""Channels""));
    boolean tasks = ""true"".equalsIgnoreCase (urlData.getParameter (""Tasks""));
    boolean systemProp = ""true"".equalsIgnoreCase (urlData.getParameter (""SystemProp""));
    boolean schedules = ""true"".equalsIgnoreCase (urlData.getParameter (""Schedules""));
    boolean authSettings = ""true"".equalsIgnoreCase (urlData.getParameter (""AuthSettings""));
    ByteArrayOutputStream bytesOut = new ByteArrayOutputStream ();
    ZipOutputStream out = new ZipOutputStream (bytesOut);
    out.setComment (""TV Scheduler Pro Settings file (Version: 1.0)"");
    if (channels) {
        out.putNextEntry (new ZipEntry (""Channels.xml""));
        StringBuffer channelData = new StringBuffer ();
        store.saveChannels (channelData);
        byte [] channelBytes = channelData.toString ().getBytes (""UTF-8"");
        out.write (channelBytes);
        out.closeEntry ();
    }
    if (matchList) {
        out.putNextEntry (new ZipEntry (""MatchList.xml""));
        StringBuffer matchData = new StringBuffer ();
        store.saveMatchList (matchData);
        byte [] matchBytes = matchData.toString ().getBytes (""UTF-8"");
        out.write (matchBytes);
        out.closeEntry ();
    }
    if (autoAdd) {
        out.putNextEntry (new ZipEntry (""EpgAutoAdd.xml""));
        StringBuffer addData = new StringBuffer ();
        store.saveEpgAutoList (addData);
        byte [] addBytes = addData.toString ().getBytes (""UTF-8"");
        out.write (addBytes);
        out.closeEntry ();
    }
    if (tasks) {
        out.putNextEntry (new ZipEntry (""Tasks.xml""));
        StringBuffer taskData = new StringBuffer ();
        store.saveTaskList (taskData);
        byte [] taskBytes = taskData.toString ().getBytes (""UTF-8"");
        out.write (taskBytes);
        out.closeEntry ();
    }
    if (channelMapping) {
        GuideStore guideStore = GuideStore.getInstance ();
        out.putNextEntry (new ZipEntry (""ChannelMap.sof""));
        ByteArrayOutputStream chanMapBytes = new ByteArrayOutputStream ();
        guideStore.saveChannelMap (chanMapBytes);
        out.write (chanMapBytes.toByteArray ());
        out.closeEntry ();
    }
    if (deviceSelection) {
        out.putNextEntry (new ZipEntry (""CaptureDevices.sof""));
        ByteArrayOutputStream deviceBytes = new ByteArrayOutputStream ();
        devList.saveDeviceList (deviceBytes);
        out.write (deviceBytes.toByteArray ());
        out.closeEntry ();
    }
    if (agentMapping) {
        out.putNextEntry (new ZipEntry (""AgentMap.sof""));
        ByteArrayOutputStream agentMapBytes = new ByteArrayOutputStream ();
        store.saveAgentToThemeMap (agentMapBytes);
        out.write (agentMapBytes.toByteArray ());
        out.closeEntry ();
    }
    if (schedules) {
        out.putNextEntry (new ZipEntry (""Times.sof""));
        ByteArrayOutputStream timesBytes = new ByteArrayOutputStream ();
        store.saveSchedule (timesBytes);
        out.write (timesBytes.toByteArray ());
        out.closeEntry ();
    }
    if (systemProp) {
        HashMap < String, String > serverProp = new HashMap < String, String > ();
        serverProp.put (""epg.showunlinked"", store.getProperty (""epg.showunlinked""));
        serverProp.put (""path.theme"", store.getProperty (""path.theme""));
        serverProp.put (""path.theme.epg"", store.getProperty (""path.theme.epg""));
        serverProp.put (""capture.path"", store.getProperty (""capture.path""));
        serverProp.put (""capture.averagedatarate"", store.getProperty (""capture.averagedatarate""));
        serverProp.put (""capture.autoselectmethod"", store.getProperty (""capture.autoselectmethod""));
        serverProp.put (""capture.minspacesoft"", store.getProperty (""capture.minspacesoft""));
        serverProp.put (""capture.includecalculatedusage"", store.getProperty (""capture.includecalculatedusage""));
        serverProp.put (""capture.deftype"", store.getProperty (""capture.deftype""));
        serverProp.put (""capture.filename.patterns"", store.getProperty (""capture.filename.patterns""));
        serverProp.put (""capture.path.details"", store.getProperty (""capture.path.details""));
        serverProp.put (""capture.capturefailedtimeout"", store.getProperty (""capture.capturefailedtimeout""));
        serverProp.put (""schedule.buffer.start"", store.getProperty (""schedule.buffer.start""));
        serverProp.put (""schedule.buffer.end"", store.getProperty (""schedule.buffer.end""));
        serverProp.put (""schedule.buffer.end.epg"", store.getProperty (""schedule.buffer.end.epg""));
        serverProp.put (""schedule.wake.system"", store.getProperty (""schedule.wake.system""));
        serverProp.put (""schedule.overlap"", store.getProperty (""schedule.overlap""));
        serverProp.put (""sch.autodel.action"", store.getProperty (""sch.autodel.action""));
        serverProp.put (""sch.autodel.time"", store.getProperty (""sch.autodel.time""));
        serverProp.put (""guide.source.http.pwd"", store.getProperty (""guide.source.http.pwd""));
        serverProp.put (""guide.source.xml.channelList"", store.getProperty (""guide.source.xml.channelList""));
        serverProp.put (""guide.source.type"", store.getProperty (""guide.source.type""));
        serverProp.put (""guide.source.http"", store.getProperty (""guide.source.http""));
        serverProp.put (""guide.source.file"", store.getProperty (""guide.source.file""));
        serverProp.put (""guide.action.name"", store.getProperty (""guide.action.name""));
        serverProp.put (""guide.source.http.usr"", store.getProperty (""guide.source.http.usr""));
        serverProp.put (""guide.source.schedule"", store.getProperty (""guide.source.schedule""));
        serverProp.put (""guide.warn.overlap"", store.getProperty (""guide.warn.overlap""));
        serverProp.put (""proxy.server"", store.getProperty (""proxy.server""));
        serverProp.put (""proxy.port"", store.getProperty (""proxy.port""));
        serverProp.put (""proxy.server.usr"", store.getProperty (""proxy.server.usr""));
        serverProp.put (""proxy.server.pwd"", store.getProperty (""proxy.server.pwd""));
        serverProp.put (""email.server"", store.getProperty (""email.server""));
        serverProp.put (""email.from.name"", store.getProperty (""email.from.name""));
        serverProp.put (""email.to"", store.getProperty (""email.to""));
        serverProp.put (""email.from"", store.getProperty (""email.from""));
        serverProp.put (""email.send.weeklyreport"", store.getProperty (""email.send.weeklyreport""));
        serverProp.put (""email.send.capfinished"", store.getProperty (""email.send.capfinished""));
        serverProp.put (""email.send.epgloaded"", store.getProperty (""email.send.epgloaded""));
        serverProp.put (""email.send.onwarning"", store.getProperty (""email.send.onwarning""));
        serverProp.put (""email.send.freespacelow"", store.getProperty (""email.send.freespacelow""));
        serverProp.put (""email.send.serverstarted"", store.getProperty (""email.send.serverstarted""));
        serverProp.put (""tasks.deftask"", store.getProperty (""tasks.deftask""));
        serverProp.put (""tasks.pretask"", store.getProperty (""tasks.pretask""));
        serverProp.put (""tasks.nodataerrortask"", store.getProperty (""tasks.nodataerrortask""));
        serverProp.put (""tasks.starterrortask"", store.getProperty (""tasks.starterrortask""));
        serverProp.put (""filebrowser.dirsattop"", store.getProperty (""filebrowser.dirsattop""));
        serverProp.put (""filebrowser.masks"", store.getProperty (""filebrowser.masks""));
        serverProp.put (""server.kbled"", store.getProperty (""server.kbled""));
        ByteArrayOutputStream serverpropBytes = new ByteArrayOutputStream ();
        ObjectOutputStream oos = new ObjectOutputStream (serverpropBytes);
        oos.writeObject (serverProp);
        oos.close ();
        out.putNextEntry (new ZipEntry (""ServerProperties.sof""));
        out.write (serverpropBytes.toByteArray ());
        out.closeEntry ();
    }
    if (authSettings) {
        File authFile = new File (store.getProperty (""path.data"") + File.separator + ""authentication.prop"");
        if (authFile.exists ()) {
            out.putNextEntry (new ZipEntry (""authentication.prop""));
            FileInputStream is = new FileInputStream (authFile);
            byte [] buff = new byte [1024];
            int read = is.read (buff);
            while (read != - 1) {
                out.write (buff, 0, read);
                read = is.read (buff);
            }
            out.closeEntry ();
            is.close ();
        }
    }
    out.flush ();
    out.close ();
    StringBuffer header = new StringBuffer ();
    header.append (""HTTP/1.1 200 OK\n"");
    header.append (""Content-Type: application/zip\n"");
    header.append (""Content-Length: "" + bytesOut.size () + ""\n"");
    header.append (""Content-Disposition: attachment; filename=\""TV Scheduler Pro Settings.zip\""\n"");
    DateFormat df = new SimpleDateFormat (""EEE, dd MMM yyyy hh:mm:ss 'GMT'"", new Locale (""En"", ""Us"", ""Unix""));
    header.append (""Last-Modified: "" + df.format (new Date ()) + ""\n"");
    header.append (""\n"");
    outStream.write (header.toString ().getBytes ());
    ByteArrayInputStream zipStream = new ByteArrayInputStream (bytesOut.toByteArray ());
    byte [] bytes = new byte [4096];
    int read = zipStream.read (bytes);
    while (read > - 1) {
        outStream.write (bytes, 0, read);
        outStream.flush ();
        read = zipStream.read (bytes);
    }
}
",21830091,"public void testImport () throws Exception {
    Init.importEverything ();
    String filename = Framework.onlyInstance ().getAppHomeDir () + ""sts-sql/example.stz"";
    ZipOutputStream zo = new ZipOutputStream (new FileOutputStream (filename));
    StringWriter swt;
    byte [] data;
    swt = new StringWriter ();
    ExportCSVRegattaWizard erw = new ExportCSVRegattaWizard (new JFrame ());
    erw.doExport (swt);
    data = swt.toString ().getBytes ();
    zo.putNextEntry (new ZipEntry (""regatta.csv""));
    zo.write (data);
    swt = new StringWriter ();
    ExportCSVEntriesWizard eew = new ExportCSVEntriesWizard (new JFrame ());
    eew.doExport (swt);
    data = swt.toString ().getBytes ();
    zo.putNextEntry (new ZipEntry (""entries.csv""));
    zo.write (data);
    swt = new StringWriter ();
    ExportCSVRaceDataWizard edw = new ExportCSVRaceDataWizard (new JFrame ());
    edw.doExport (swt);
    data = swt.toString ().getBytes ();
    zo.putNextEntry (new ZipEntry (""race-data.csv""));
    zo.write (data);
    zo.close ();
}
",Zip Files,Type-3 (WT3/4),TRUE
233637,"public void service (HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
    ServletContext context = getServletContext ();
    String forw = null;
    try {
        int maxUploadSize = 50000000;
        MultipartRequest multi = new MultipartRequest (request, ""."", maxUploadSize);
        String descrizione = multi.getParameter (""text"");
        File myFile = multi.getFile (""uploadfile"");
        String filePath = multi.getOriginalFileName (""uploadfile"");
        String path = ""C:\\files\\"";
        try {
            FileInputStream inStream = new FileInputStream (myFile);
            FileOutputStream outStream = new FileOutputStream (path + myFile.getName ());
            while (inStream.available () > 0) {
                outStream.write (inStream.read ());
            }
            inStream.close ();
            outStream.close ();
        } catch (FileNotFoundException fnfe) {
            fnfe.printStackTrace ();
        } catch (IOException ioe) {
            ioe.printStackTrace ();
        }
        forw = ""../sendDoc.jsp"";
        request.setAttribute (""contentType"", context.getMimeType (path + myFile.getName ()));
        request.setAttribute (""text"", descrizione);
        request.setAttribute (""path"", path + myFile.getName ());
        request.setAttribute (""size"", Long.toString (myFile.length ()) + "" Bytes"");
        RequestDispatcher rd = request.getRequestDispatcher (forw);
        rd.forward (request, response);
    } catch (Exception e) {
        e.printStackTrace ();
    }
}
",21931071,"public static void writeToPetrify (TransitionSystem ts, Writer bw) throws IOException {
    File temp = new File (""_temp"");
    BufferedWriter tw = new BufferedWriter (new FileWriter (temp));
    BufferedReader tr = new BufferedReader (new FileReader (temp));
    HashSet < ModelGraphVertex > sources = new HashSet < ModelGraphVertex > ();
    HashSet < ModelGraphVertex > dests = new HashSet < ModelGraphVertex > ();
    ArrayList transitions = ts.getEdges ();
    HashSet < String > events = new HashSet < String > ();
    for (int i = 0;
    i < transitions.size (); i ++) {
        TransitionSystemEdge transition = (TransitionSystemEdge) transitions.get (i);
        events.add (replaceBadSymbols (transition.getIdentifier ()));
        sources.add (transition.getSource ());
        dests.add (transition.getDest ());
        if (ts.getStateNameFlag () == TransitionSystem.ID) {
            tw.write (""s"" + transition.getSource ().getId () + "" "");
            tw.write (replaceBadSymbols (transition.getIdentifier ()) + "" "");
            tw.write (""s"" + transition.getDest ().getId () + ""\n"");
        } else {
            tw.write (replaceBadSymbols (transition.getSource ().getIdentifier ()) + "" "");
            tw.write (replaceBadSymbols (transition.getIdentifier ()) + "" "");
            tw.write (replaceBadSymbols (transition.getDest ().getIdentifier ()) + ""\n"");
        }
    }
    tw.close ();
    bw.write ("".model "" + ts.getName ().replaceAll ("" "", ""_"") + ""\n"");
    bw.write ("".dummy "");
    Iterator it = events.iterator ();
    while (it.hasNext ()) bw.write (it.next () + "" "");

    bw.write (""\n"");
    bw.write ("".state graph"" + ""\n"");
    int c;
    while ((c = tr.read ()) != - 1) bw.write (c);

    tr.close ();
    temp.delete ();
    for (ModelGraphVertex dest : dests) {
        if (sources.contains (dest)) {
            sources.remove (dest);
        }
    }
    ModelGraphVertex source = sources.isEmpty () ? null : sources.iterator ().next ();
    if (ts.getStateNameFlag () == TransitionSystem.ID) {
        if (! ts.hasExplicitEnd ()) bw.write ("".marking {s0}"" + ""\n"");
        else bw.write ("".marking {s"" + source.getId () + ""}\n"");

    } else if (source != null) {
        bw.write ("".marking {"" + replaceBadSymbols (source.getIdentifier ()) + ""}\n"");
    }

    bw.write ("".end"");
}
",Copy File,Type-3 (WT3/4),TRUE
2049240,"private void writeInfos () throws IOException {
    zos.putNextEntry (new ZipEntry (""info.bin""));
    outFile = new DataOutputStream (zos);
    outFile.writeInt (VERSION);
    outFile.writeInt (MINORVERSION);
    outFile.writeDouble (intervall_s);
    zos.closeEntry ();
}
",20339695,"private void addToZip (String path, String srcFile, ZipOutputStream zip) {
    File folder = new File (srcFile);
    if (folder.isDirectory ()) {
        this.addFolderToZip (path, srcFile, zip);
    } else {
        try {
            boolean includeFile = false;
            if (this.excludePattern == null) {
                includeFile = true;
            } else {
                if (srcFile.contains (this.excludePattern)) {
                    includeFile = false;
                } else {
                    includeFile = true;
                }
            }
            if (includeFile == true) {
                this.zipMonitor.setNumberNextFile ();
                this.zipMonitor.setCurrentJobFile (srcFile);
                if (zipMonitor.isCanceled ()) {
                    return;
                }
                FileInputStream in = new FileInputStream (srcFile);
                zip.putNextEntry (new ZipEntry (path + File.separator + folder.getName ()));
                byte [] buf = new byte [1024];
                int len;
                while ((len = in.read (buf)) > 0) {
                    zip.write (buf, 0, len);
                }
            }
        } catch (Exception ex) {
            ex.printStackTrace ();
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
1803586,"private Service getServiceInstance (String className) {
    try {
        Class clazz = Class.forName (className);
        return (Service) clazz.getConstructor (new Class [] {}).newInstance (new Object [] {});
    } catch (ClassNotFoundException e) {
        this.logger.error (className, e);
        return null;
    } catch (SecurityException e) {
        this.logger.error (className, e);
        return null;
    } catch (NoSuchMethodException e) {
        this.logger.error (className, e);
        return null;
    } catch (IllegalArgumentException e) {
        this.logger.error (className, e);
        return null;
    } catch (InstantiationException e) {
        this.logger.error (className, e);
        return null;
    } catch (IllegalAccessException e) {
        this.logger.error (className, e);
        return null;
    } catch (InvocationTargetException e) {
        this.logger.error (className, e);
        return null;
    }
}
",1849134,"private void setCommandInput () {
    mCommandInput = null;
    try {
        Class < ? > consoleReaderClass = Class.forName (""jline.ConsoleReader"");
        if (consoleReaderClass != null) {
            Class < ? > consoleInputClass = Class.forName (""jline.ConsoleReaderInputStream"");
            if (consoleInputClass != null) {
                Object jline = consoleReaderClass.newInstance ();
                Constructor < ? > constructor = consoleInputClass.getConstructor (consoleReaderClass);
                if (constructor != null) {
                    mCommandInput = (InputStream) constructor.newInstance (jline);
                }
            }
        }
    } catch (Exception e1) {
        mLogger.info (""Exception loading jline"");
    }
    if (mCommandInput == null) mCommandInput = System.in;

}
",Instantiate Using Reflection,Type-3 (WT3/4),TRUE
7885446,"public static String CreateZip (String [] filesToZip, String zipFileName) {
    byte [] buffer = new byte [18024];
    try {
        ZipOutputStream out = new ZipOutputStream (new FileOutputStream (zipFileName));
        out.setLevel (Deflater.BEST_COMPRESSION);
        for (int i = 0;
        i < filesToZip.length; i ++) {
            FileInputStream in = new FileInputStream (filesToZip [i]);
            String fileName = null;
            for (int X = filesToZip [i].length () - 1;
            X >= 0; X --) {
                if (filesToZip [i].charAt (X) == '\\' || filesToZip [i].charAt (X) == '/') {
                    fileName = filesToZip [i].substring (X + 1);
                    break;
                } else if (X == 0) fileName = filesToZip [i];

            }
            out.putNextEntry (new ZipEntry (fileName));
            int len;
            while ((len = in.read (buffer)) > 0) out.write (buffer, 0, len);

            out.closeEntry ();
            in.close ();
        }
        out.close ();
    } catch (IllegalArgumentException e) {
        return ""Failed to create zip: "" + e.toString ();
    } catch (FileNotFoundException e) {
        return ""Failed to create zip: "" + e.toString ();
    } catch (IOException e) {
        return ""Failed to create zip: "" + e.toString ();
    }
    return ""Success"";
}
",17792212,"private void createButtonCopyToClipboard () {
    buttonCopyToClipboard = new Button (shell, SWT.PUSH);
    buttonCopyToClipboard.setText (""Co&py to Clipboard"");
    buttonCopyToClipboard.setLayoutData (SharedStyle.relativeToBottomRight (buttonClose));
    buttonCopyToClipboard.addSelectionListener (new SelectionAdapter () {
        @Override
        public void widgetSelected (final SelectionEvent event) {
            IOUtils.copyToClipboard (Version.getEnvironmentReport ());
        }}

    );
}
",Copy File,Type-3 (WT3/4),TRUE
16166059,"public void transform (File inputMatrixFile, MatrixIO.Format inputFormat, File outputMatrixFile) throws IOException {
    FileChannel original = new FileInputStream (inputMatrixFile).getChannel ();
    FileChannel copy = new FileOutputStream (outputMatrixFile).getChannel ();
    copy.transferFrom (original, 0, original.size ());
    original.close ();
    copy.close ();
}
",22224116,"public static void main (String [] args) throws IOException {
    if (args.length == 0) {
        System.out.println (""Usage: \nGZIPcompress file\n"" + ""\tUses GZIP compression to compress "" + ""the file to test.gz"");
        System.exit (1);
    }
    BufferedReader in = new BufferedReader (new FileReader (args [0]));
    BufferedOutputStream out = new BufferedOutputStream (new GZIPOutputStream (new FileOutputStream (""test.gz"")));
    System.out.println (""Writing file"");
    int c;
    while ((c = in.read ()) != - 1) out.write (c);

    in.close ();
    out.close ();
    System.out.println (""Reading file"");
    BufferedReader in2 = new BufferedReader (new InputStreamReader (new GZIPInputStream (new FileInputStream (""test.gz""))));
    String s;
    while ((s = in2.readLine ()) != null) System.out.println (s);

}
",Copy File,Type-3 (WT3/4),TRUE
1189377,"private < T extends APIObject > T executeApi (Class < T > returnclass, List < NameValuePair > getParams, List < NameValuePair > postParams) throws WikimediaApiException {
    ArrayList < NameValuePair > gets = new ArrayList < NameValuePair > (defaultparams);
    if (getParams != null) gets.addAll (getParams);

    gets.add (new BasicNameValuePair (""requestid"", """" + requestCounter ++));
    String getParamString = URLEncodedUtils.format (gets, ""utf-8"");
    HttpUriRequest req = postParams == null ? new HttpGet (apiurl + ""?"" + getParamString) : new HttpPost (apiurl + ""?"" + getParamString);
    if (postParams != null) try {
        ((HttpPost) req).setEntity (new UrlEncodedFormEntity (postParams));
    } catch (UnsupportedEncodingException e) {
        throw new WikimediaApiException (""IOError"", e);
    }

    try {
        BufferedReader in = new BufferedReader (new InputStreamReader (execute (req).getEntity ().getContent ()));
        String line = in.readLine ();
        T obj = returnclass.getConstructor (String.class).newInstance (line);
        if (obj.has (""error"")) {
            JSONObject err = (JSONObject) obj.get (""error"");
            throw new WikimediaApiException (err.get (""code"") + "": "" + err.get (""info""));
        }
        return obj;
    } catch (Exception exc) {
        throw new RuntimeException (exc);
    }
}
",2234608,"@SuppressWarnings(""unchecked"")
@Transactional(readOnly=true)
public Map < String, Object > getParameterValues (Map < String, String [] > requestParams, InputStream reportFile) {
    Map < String, Object > ret = new HashMap < String, Object > ();
    try {
        SAXReader saxReader = new SAXReader ();
        Document document = saxReader.read (reportFile);
        List < Element > list = document.getRootElement ().elements (""parameter"");
        for (String param : requestParams.keySet ()) {
            if (DynamicReport.REPORT_FILE.equals (param) || DynamicReport.REPORT_FORMAT.equals (param)) continue;

            for (Element elem : list) {
                Attribute attrib = elem.attribute (""name"");
                if (attrib.getValue ().equals (param)) {
                    Attribute attrClass = elem.attribute (""class"");
                    String className = ""java.lang.String"";
                    String [] valueArr = requestParams.get (param);
                    String value = StringUtil.explode (',', valueArr);
                    if (StringUtil.isEmpty (value)) continue;

                    if (attrClass != null) className = attrClass.getValue ();

                    try {
                        if (""java.io.InputStream"".equals (className)) {
                            File image = new File (jasperPath + value);
                            InputStream stream = new FileInputStream (image);
                            if (stream == null) _log.warn (""Unable to find file ["" + jasperPath + value + ""]"");
                            else ret.put (param, stream);

                        } else if (""java.util.List"".equals (className)) {
                            if (value != null) {
                                String [] values = value.split ("","");
                                List < String > temp = Arrays.asList (values);
                                ret.put (param, temp);
                            }
                        } else {
                            Class classDefinition = Class.forName (className);
                            Object objectValue = classDefinition.getConstructor (String.class).newInstance (value);
                            ret.put (param, objectValue);
                        }

                    } catch (Exception e) {
                        _log.error (""Failed to parse parameter ["" + param + ""] with value ["" + value + ""]."", e);
                    }
                }
            }
        }
    } catch (DocumentException e) {
        _log.error (e, e);
    }
    return ret;
}
",Instantiate Using Reflection,Type-3 (WT3/4),TRUE
1039796,"public static void insert (Connection c, MLPApprox net, int azioneId, String descrizione, int [] indiciID, int output, Date from, Date to) throws SQLException {
    try {
        PreparedStatement ps = c.prepareStatement (insertNet, PreparedStatement.RETURN_GENERATED_KEYS);
        ArrayList < Integer > indexes = new ArrayList < Integer > (indiciID.length);
        for (int i = 0;
        i < indiciID.length; i ++) indexes.add (indiciID [i]);

        ps.setObject (1, net);
        ps.setInt (2, azioneId);
        ps.setObject (3, indexes);
        ps.setInt (4, output);
        ps.setDate (5, from);
        ps.setDate (6, to);
        ps.setString (7, descrizione);
        ps.executeUpdate ();
        ResultSet key = ps.getGeneratedKeys ();
        if (key.next ()) {
            int id = key.getInt (1);
            for (int i = 0;
            i < indiciID.length; i ++) {
                PreparedStatement psIndex = c.prepareStatement (insertNetIndex);
                psIndex.setInt (1, indiciID [i]);
                psIndex.setInt (2, id);
                psIndex.executeUpdate ();
            }
        }
    } catch (SQLException e) {
        e.printStackTrace ();
        try {
            c.rollback ();
        } catch (SQLException e1) {
            e1.printStackTrace ();
            throw e1;
        }
        throw e;
    }
}
",19147297,"public boolean ponerRivalxRonda (int idJugadorDiv, int idRonda, int dato) {
    int intResult = 0;
    String sql = ""UPDATE jugadorxdivxronda "" + "" SET idPareoRival = "" + dato + "" WHERE jugadorxDivision_idJugadorxDivision = "" + idJugadorDiv + "" AND ronda_numeroRonda = "" + idRonda;
    try {
        connection = conexionBD.getConnection ();
        connection.setAutoCommit (false);
        ps = connection.prepareStatement (sql);
        intResult = ps.executeUpdate ();
        connection.commit ();
    } catch (SQLException ex) {
        ex.printStackTrace ();
        try {
            connection.rollback ();
        } catch (SQLException exe) {
            exe.printStackTrace ();
        }
    } finally {
        conexionBD.close (ps);
        conexionBD.close (connection);
    }
    return (intResult > 0);
}
",Execute update and rollback.,Type-3 (WT3/4),TRUE
1086128,"public void streamDataToZip (VolumeTimeSeries vol, ZipOutputStream zout) throws Exception {
    ZipEntry entry = new ZipEntry (vol.getId () + "".dat"");
    zout.putNextEntry (entry);
    if (vol instanceof FloatVolumeTimeSeries) {
        streamData (((FloatVolumeTimeSeries) vol).getData (), zout);
    } else if (vol instanceof RGBVolumeTimeSeries) {
        streamData (((RGBVolumeTimeSeries) vol).getARGBData (), zout);
    } else if (vol instanceof BinaryVolumeTimeSeries) {
        streamData (((BinaryVolumeTimeSeries) vol).getBinaryData (), zout);
    }

}
",17886809,"private void zipDir (String baseDir, String dir2zip, ZipOutputStream zos) throws IOException {
    File zipDir = new File (dir2zip);
    String [] dirList = zipDir.list ();
    for (int i = 0;
    i < dirList.length; i ++) {
        File f = new File (zipDir, dirList [i]);
        if (f.isDirectory ()) {
            String filePath = f.getPath ();
            zipDir (baseDir, filePath, zos);
        } else {
            FileInputStream fis = new FileInputStream (f);
            String basePath = new File (baseDir).getCanonicalPath ();
            String entryName = f.getCanonicalPath ();
            if (entryName.length () > basePath.length ()) entryName = entryName.substring (basePath.length () + 1);

            ZipEntry anEntry = new ZipEntry (entryName);
            zos.putNextEntry (anEntry);
            byte [] readBuffer = new byte [512];
            int bytesIn = 0;
            while ((bytesIn = fis.read (readBuffer)) != - 1) {
                zos.write (readBuffer, 0, bytesIn);
            }
            fis.close ();
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
2415606,"public void updateVal (Configuration config) {
    updateValSuper (config);
    String value = field.getText ();
    Class [] params = new Class [1];
    Object [] args = new Object [1];
    params [0] = String.class;
    args [0] = value;
    Object o = null;
    try {
        Constructor c = mObj.getClass ().getConstructor (params);
        o = c.newInstance (args);
    } catch (Exception ex) {
        throw new IllegalStateException (""Problem writing unknown class to configuration"");
    }
    config.put (key, o);
}
",3343774,"public < T extends Unit > T buildNewUnit (String propertiesFile, Class < T > unitType) throws Exception {
    Constructor < T > constructor = unitType.getConstructor (String.class);
    T newUnit = constructor.newInstance (propertiesFile);
    units.add (newUnit);
    return newUnit;
}
",Instantiate Using Reflection,Type-3 (WT3/4),TRUE
1184290,"@Override
public void execute () {
    File currentModelDirectory = new File (this.globalData.getData (String.class, GlobalData.MODEL_INSTALL_DIRECTORY));
    File mobileDirectory = new File (currentModelDirectory, ""mobile"");
    mobileDirectory.mkdir ();
    File mobileModelFile = new File (mobileDirectory, ""mobile_model.zip"");
    FileOutputStream outputStream = null;
    ZipOutputStream zipStream = null;
    BusinessModel businessModel = BusinessUnit.getInstance ().getBusinessModel ();
    try {
        mobileModelFile.createNewFile ();
        outputStream = new FileOutputStream (mobileModelFile);
        zipStream = new ZipOutputStream (outputStream);
        Dictionary dictionary = businessModel.getDictionary ();
        for (Definition definition : dictionary.getAllDefinitions ()) {
            ZipEntry entry = new ZipEntry (definition.getRelativeFileName ());
            zipStream.putNextEntry (entry);
            writeBinary (definition.getAbsoluteFileName (), zipStream);
        }
        final String modelFilename = ""model.xml"";
        ZipEntry entry = new ZipEntry (modelFilename);
        zipStream.putNextEntry (entry);
        writeBinary (businessModel.getAbsoluteFilename (modelFilename), zipStream);
        final String logoFilename = dictionary.getModel ().getImageSource (LogoType.mobile);
        entry = new ZipEntry (logoFilename);
        zipStream.putNextEntry (entry);
        writeBinary (businessModel.getAbsoluteFilename (logoFilename), zipStream);
    } catch (IOException e) {
        agentLogger.error (e);
    } finally {
        StreamHelper.close (zipStream);
        StreamHelper.close (outputStream);
    }
}
",3974027,"private void addTopicToZip (ZipOutputStream zipout, HashMap containingTopics, SearchEngine sedb, String defaultTopic, List ignoreTheseTopicsList, String topicname) throws Exception, IOException {
    WikiBase wb = WikiBase.getInstance ();
    Template tpl;
    tpl = new Template (this.getServletContext ().getRealPath (""/WEB-INF/classes/export2html/mastertemplate.tpl""));
    tpl.setFieldGlobal (""VERSION"", WikiBase.WIKI_VERSION);
    StringBuffer oneline = new StringBuffer ();
    if (! ignoreTheseTopicsList.contains (topicname)) {
        oneline.append (topicname);
        tpl.setFieldGlobal (""TOPICNAME"", topicname);
        Topic topicObject = new Topic (topicname);
        logger.debug (""Adding topic "" + topicname);
        String author = null;
        java.util.Date lastRevisionDate = null;
        if (Environment.getBooleanValue (Environment.PROP_TOPIC_VERSIONING_ON)) {
            lastRevisionDate = topicObject.getMostRecentRevisionDate (virtualWiki);
            author = topicObject.getMostRecentAuthor (virtualWiki);
            if (author != null || lastRevisionDate != null) {
                tpl.setField (""SHOWVERSIONING1"", ""-->"");
                if (author != null) tpl.setField (""AUTHOR"", author);

                if (lastRevisionDate != null) tpl.setField (""MODIFYDATE"", Utilities.formatDate (lastRevisionDate));

                tpl.setField (""SHOWVERSIONING2"", ""<!--"");
            }
        }
        StringBuffer content = new StringBuffer ();
        content.append (Topic.readCooked (virtualWiki, topicname, Environment.getValue (Environment.PROP_PARSER_FORMAT_LEXER), Environment.getValue (Environment.PROP_PARSER_LAYOUT_LEXER), ""vqwiki.lex.HTMLLinkLex"", true));
        String redirect = ""redirect:"";
        if (content.toString ().startsWith (redirect)) {
            StringBuffer link = new StringBuffer (content.toString ().substring (redirect.length ()).trim ());
            while (link.toString ().indexOf (""<"") != - 1) {
                int startpos = link.toString ().indexOf (""<"");
                int endpos = link.toString ().indexOf ("">"");
                if (endpos == - 1) {
                    endpos = link.length ();
                } else {
                    endpos ++;
                }
                link.delete (startpos, endpos);
            }
            link = new StringBuffer (safename (link.toString ().trim ()));
            link = link.append ("".html"");
            String nl = System.getProperty (""line.separator"");
            tpl.setFieldGlobal (""REDIRECT"", ""<script>"" + nl + ""location.replace(\"""" + link.toString () + ""\"");"" + nl + ""</script>"" + nl + ""<meta http-equiv=\""refresh\"" content=\""1; "" + link.toString () + ""\"">"" + nl);
        } else {
            tpl.setFieldGlobal (""REDIRECT"", """");
        }
        Collection searchresult = sedb.find (virtualWiki, topicname, false);
        if (searchresult != null && searchresult.size () > 0) {
            Iterator it = searchresult.iterator ();
            String divider = """";
            StringBuffer backlinks = new StringBuffer ();
            for (; it.hasNext ();) {
                SearchResultEntry result = (SearchResultEntry) it.next ();
                if (! result.getTopic ().equals (topicname)) {
                    backlinks.append (divider);
                    backlinks.append (""<a href=\"""");
                    backlinks.append (safename (result.getTopic ()));
                    backlinks.append ("".html\"">"");
                    backlinks.append (result.getTopic ());
                    backlinks.append (""</a>"");
                    divider = "" | "";
                    List l = (List) containingTopics.get (result.getTopic ());
                    if (l == null) {
                        l = new ArrayList ();
                    }
                    if (! l.contains (topicname)) {
                        l.add (topicname);
                    }
                    containingTopics.put (result.getTopic (), l);
                }
            }
            if (backlinks.length () > 0) {
                ResourceBundle messages = ResourceBundle.getBundle (""ApplicationResources"", locale);
                content.append (""<br /><br /><span class=\""backlinks\"">"");
                content.append (topicname);
                content.append ("" "");
                content.append (messages.getString (""topic.ismentionedon""));
                content.append ("" "");
                content.append (backlinks.toString ());
                content.append (""</span>"");
            }
        }
        tpl.setFieldGlobal (""CONTENTS"", content.toString ());
        ZipEntry entry = new ZipEntry (safename (topicname) + "".html"");
        StringReader in = new StringReader (tpl.getContent ());
        zipout.putNextEntry (entry);
        int read = 0;
        while ((read = in.read ()) != - 1) {
            zipout.write (read);
        }
        zipout.closeEntry ();
        zipout.flush ();
        if (topicname.equals (defaultTopic)) {
            entry = new ZipEntry (""index.html"");
            in = new StringReader (tpl.getContent ());
            zipout.putNextEntry (entry);
            read = 0;
            while ((read = in.read ()) != - 1) {
                zipout.write (read);
            }
            zipout.closeEntry ();
            zipout.flush ();
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
340064,"public void convert (File src, File dest) throws IOException {
    InputStream in = new BufferedInputStream (new FileInputStream (src));
    DcmParser p = pfact.newDcmParser (in);
    Dataset ds = fact.newDataset ();
    p.setDcmHandler (ds.getDcmHandler ());
    try {
        FileFormat format = p.detectFileFormat ();
        if (format != FileFormat.ACRNEMA_STREAM) {
            System.out.println (""\n"" + src + "": not an ACRNEMA stream!"");
            return;
        }
        p.parseDcmFile (format, Tags.PixelData);
        if (ds.contains (Tags.StudyInstanceUID) || ds.contains (Tags.SeriesInstanceUID) || ds.contains (Tags.SOPInstanceUID) || ds.contains (Tags.SOPClassUID)) {
            System.out.println (""\n"" + src + "": contains UIDs!"" + "" => probable already DICOM - do not convert"");
            return;
        }
        boolean hasPixelData = p.getReadTag () == Tags.PixelData;
        boolean inflate = hasPixelData && ds.getInt (Tags.BitsAllocated, 0) == 12;
        int pxlen = p.getReadLength ();
        if (hasPixelData) {
            if (inflate) {
                ds.putUS (Tags.BitsAllocated, 16);
                pxlen = pxlen * 4 / 3;
            }
            if (pxlen != (ds.getInt (Tags.BitsAllocated, 0)>>> 3) * ds.getInt (Tags.Rows, 0) * ds.getInt (Tags.Columns, 0) * ds.getInt (Tags.NumberOfFrames, 1) * ds.getInt (Tags.NumberOfSamples, 1)) {
                System.out.println (""\n"" + src + "": mismatch pixel data length!"" + "" => do not convert"");
                return;
            }
        }
        ds.putUI (Tags.StudyInstanceUID, uid (studyUID));
        ds.putUI (Tags.SeriesInstanceUID, uid (seriesUID));
        ds.putUI (Tags.SOPInstanceUID, uid (instUID));
        ds.putUI (Tags.SOPClassUID, classUID);
        if (! ds.contains (Tags.NumberOfSamples)) {
            ds.putUS (Tags.NumberOfSamples, 1);
        }
        if (! ds.contains (Tags.PhotometricInterpretation)) {
            ds.putCS (Tags.PhotometricInterpretation, ""MONOCHROME2"");
        }
        if (fmi) {
            ds.setFileMetaInfo (fact.newFileMetaInfo (ds, UIDs.ImplicitVRLittleEndian));
        }
        OutputStream out = new BufferedOutputStream (new FileOutputStream (dest));
        try {
        } finally {
            ds.writeFile (out, encodeParam ());
            if (hasPixelData) {
                if (! skipGroupLen) {
                    out.write (PXDATA_GROUPLEN);
                    int grlen = pxlen + 8;
                    out.write ((byte) grlen);
                    out.write ((byte) (grlen>> 8));
                    out.write ((byte) (grlen>> 16));
                    out.write ((byte) (grlen>> 24));
                }
                out.write (PXDATA_TAG);
                out.write ((byte) pxlen);
                out.write ((byte) (pxlen>> 8));
                out.write ((byte) (pxlen>> 16));
                out.write ((byte) (pxlen>> 24));
            }
            if (inflate) {
                int b2, b3;
                for (; pxlen > 0; pxlen -= 3) {
                    out.write (in.read ());
                    b2 = in.read ();
                    b3 = in.read ();
                    out.write (b2 & 0x0f);
                    out.write (b2>> 4 | ((b3 & 0x0f) << 4));
                    out.write (b3>> 4);
                }
            } else {
                for (; pxlen > 0; -- pxlen) {
                    out.write (in.read ());
                }
            }
            out.close ();
        }
        System.out.print ('.');
    } finally {
        in.close ();
    }
}
",413620,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",Copy File,Type-3 (WT3/4),TRUE
555528,"public static long compute (String str) {
    CRC32 crc = new CRC32 ();
    Adler32 adler = new Adler32 ();
    crc.update (str.getBytes ());
    adler.update (str.getBytes ());
    long dg1 = crc.getValue ();
    long dg2 = adler.getValue ();
    crc.update (String.valueOf (dg2).getBytes ());
    adler.update (String.valueOf (dg1).getBytes ());
    long d3 = crc.getValue ();
    long d4 = adler.getValue ();
    dg1 ^= d4;
    dg2 ^= d3;
    return (dg2 ^ ((dg1>>> 32) | (dg1 << 32)));
}
",16506879,"private static long crc32 (byte [] stream) {
    CRC32 crc32 = new CRC32 ();
    crc32.reset ();
    crc32.update (stream);
    long res = crc32.getValue ();
    return res;
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
8248731,"public static void copy (File source, File dest) throws BuildException {
    dest = new File (dest, source.getName ());
    if (source.isFile ()) {
        byte [] buffer = new byte [4096];
        FileInputStream fin = null;
        FileOutputStream fout = null;
        try {
            fin = new FileInputStream (source);
            fout = new FileOutputStream (dest);
            int count = 0;
            while ((count = fin.read (buffer)) > 0) fout.write (buffer, 0, count);

            fin.close ();
            fout.close ();
        } catch (IOException ex) {
            throw new BuildException (ex);
        } finally {
            try {
                if (fin != null) fin.close ();

            } catch (IOException ex) {
            }
            try {
                if (fout != null) fout.close ();

            } catch (IOException ex) {
            }
        }
    } else {
        dest.mkdirs ();
        File [] children = source.listFiles ();
        for (File child : children) copy (child, dest);

    }
}
",18488108,"public static void saveZipComponents (ZipComponents zipComponents, File zipFile) throws FileNotFoundException, IOException, Exception {
    ZipOutputStream zipOutStream = new ZipOutputStream (new FileOutputStream (zipFile));
    for (ZipComponent comp : zipComponents.getComponents ()) {
        ZipEntry newEntry = new ZipEntry (comp.getName ());
        zipOutStream.putNextEntry (newEntry);
        if (comp.isDirectory ()) {
        } else {
            if (comp.getName ().endsWith (""document.xml"") || comp.getName ().endsWith (""document.xml.rels"")) {
            }
            InputStream inputStream = comp.getInputStream ();
            IOUtils.copy (inputStream, zipOutStream);
            inputStream.close ();
        }
    }
    zipOutStream.close ();
}
",Copy File,Type-3 (WT3/4),TRUE
1514106,"private void exportLearningUnitView (File selectedFile) {
    if (learningUnitViewElementsManager.isOriginalElementsOnly ()) {
        String [] elementIds = learningUnitViewElementsManager.getAllLearningUnitViewElementIds ();
        for (int i = 0;
        i < elementIds.length; i ++) {
            FSLLearningUnitViewElement element = learningUnitViewElementsManager.getLearningUnitViewElement (elementIds [i], false);
            if (element.getLastModificationDate () == null) {
                element.setLastModificationDate (String.valueOf (new Date ().getTime ()));
                element.setModified (true);
            }
        }
        learningUnitViewElementsManager.setModified (true);
        learningUnitViewManager.saveLearningUnitViewData ();
        if (selectedFile != null) {
            try {
                File outputFile = selectedFile;
                String fileName = outputFile.getName ();
                StringBuffer extension = new StringBuffer ();
                if (fileName.length () >= 5) {
                    for (int i = 5;
                    i > 0; i --) {
                        extension.append (fileName.charAt (fileName.length () - i));
                    }
                }
                if (! extension.toString ().equals ("".fslv"")) {
                    outputFile.renameTo (new File (outputFile.getAbsolutePath () + "".fslv""));
                    outputFile = new File (outputFile.getAbsolutePath () + "".fslv"");
                }
                File files [] = selectedFile.getParentFile ().listFiles ();
                int returnValue = FLGOptionPane.OK_OPTION;
                for (int i = 0;
                i < files.length; i ++) {
                    if (outputFile.getAbsolutePath ().equals (files [i].getAbsolutePath ())) {
                        returnValue = FLGOptionPane.showConfirmDialog (internationalization.getString (""dialog.exportLearningUnitView.fileExits.message""), internationalization.getString (""dialog.exportLearningUnitView.fileExits.title""), FLGOptionPane.OK_CANCEL_OPTION, FLGOptionPane.QUESTION_MESSAGE);
                        break;
                    }
                }
                if (returnValue == FLGOptionPane.OK_OPTION) {
                    FileOutputStream os = new FileOutputStream (outputFile);
                    ZipOutputStream zipOutputStream = new ZipOutputStream (os);
                    ZipEntry zipEntry = new ZipEntry (""dummy"");
                    zipOutputStream.putNextEntry (zipEntry);
                    zipOutputStream.closeEntry ();
                    zipOutputStream.flush ();
                    zipOutputStream.finish ();
                    zipOutputStream.close ();
                    final File outFile = outputFile;
                    (new Thread () {
                        public void run () {
                            try {
                                ZipOutputStream zipOutputStream = new ZipOutputStream (new FileOutputStream (outFile));
                                File [] files = (new File (learningUnitViewManager.getLearningUnitViewOriginalDataDirectory ().getPath ())).listFiles ();
                                int maxSteps = files.length;
                                int step = 1;
                                exportProgressDialog = new FLGImageProgressDialog (null, 0, maxSteps, 0, getClass ().getClassLoader ().getResource (""freestyleLearning/homeCore/images/fsl.gif""), (Color) UIManager.get (""FSLColorBlue""), (Color) UIManager.get (""FSLColorRed""), internationalization.getString (""learningUnitViewExport.rogressbarText""));
                                exportProgressDialog.setCursor (new Cursor (Cursor.WAIT_CURSOR));
                                exportProgressDialog.setBarValue (step);
                                buildExportZipFile ("""", zipOutputStream, files, step);
                                zipOutputStream.flush ();
                                zipOutputStream.finish ();
                                zipOutputStream.close ();
                                exportProgressDialog.setBarValue (maxSteps);
                                exportProgressDialog.setCursor (new Cursor (Cursor.DEFAULT_CURSOR));
                                exportProgressDialog.dispose ();
                            } catch (Exception e) {
                                e.printStackTrace ();
                            }
                        }}

                    ).start ();
                    os.close ();
                }
            } catch (Exception exp) {
                exp.printStackTrace ();
            }
        }
    } else {
    }
}
",4220140,"protected void addFile (File newEntry, String name) {
    if (newEntry.isDirectory ()) {
        return;
    }
    try {
        ZipEntry ze = new ZipEntry (name);
        mZos.putNextEntry (ze);
        FileInputStream fis = new FileInputStream (newEntry);
        byte fdata [] = new byte [512];
        int readCount = 0;
        while ((readCount = fis.read (fdata)) != - 1) {
            mZos.write (fdata, 0, readCount);
        }
        fis.close ();
        mZos.closeEntry ();
        mObserverCont.setNext (ze);
        mObserverCont.setCount (++ miCurrentCount);
    } catch (Exception ex) {
        mObserverCont.setError (ex.getMessage ());
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
701471,"private boolean enregistreToi () {
    PrintWriter lEcrivain;
    String laDest = ""./img_types/"" + sonImage;
    if (! new File (""./img_types"").exists ()) {
        new File (""./img_types"").mkdirs ();
    }
    try {
        FileChannel leFicSource = new FileInputStream (sonFichier).getChannel ();
        FileChannel leFicDest = new FileOutputStream (laDest).getChannel ();
        leFicSource.transferTo (0, leFicSource.size (), leFicDest);
        leFicSource.close ();
        leFicDest.close ();
        lEcrivain = new PrintWriter (new FileWriter (new File (""bundll/types.jay""), true));
        lEcrivain.println (sonNom);
        lEcrivain.println (sonImage);
        if (sonOptionRadio1.isSelected ()) {
            lEcrivain.println (""0:?"");
        }
        if (sonOptionRadio2.isSelected ()) {
            lEcrivain.println (""1:"" + JOptionPane.showInputDialog (null, ""Vous avez choisis de rendre ce terrain difficile � franchir.\nVeuillez en indiquer la raison."", ""Demande de pr�cision"", JOptionPane.INFORMATION_MESSAGE));
        }
        if (sonOptionRadio3.isSelected ()) {
            lEcrivain.println (""2:?"");
        }
        lEcrivain.close ();
        return true;
    } catch (Exception lException) {
        return false;
    }
}
",9257486,"public static boolean dumpFile (String from, File to, String lineBreak) {
    try {
        BufferedReader in = new BufferedReader (new InputStreamReader (new FileInputStream (from)));
        BufferedWriter out = new BufferedWriter (new OutputStreamWriter (new FileOutputStream (to)));
        String line = null;
        while ((line = in.readLine ()) != null) out.write (Main.getInstance ().resolve (line) + lineBreak);

        in.close ();
        out.close ();
    } catch (Exception e) {
        Installer.getInstance ().getLogger ().log (StringUtils.getStackTrace (e));
        return false;
    }
    return true;
}
",Copy File,Type-3 (WT3/4),TRUE
13361852,"public static File copyFile (File from, File to) throws IOException {
    FileOutputStream fos = new FileOutputStream (to);
    FileInputStream fis = new FileInputStream (from);
    FileChannel foc = fos.getChannel ();
    FileChannel fic = fis.getChannel ();
    foc.transferFrom (fic, 0, fic.size ());
    foc.close ();
    fic.close ();
    return to;
}
",20326462,"public void bindDownload (Download download) throws BindingException {
    List < ChunkDownload > chunks = download.getChunks ();
    File destination = download.getFile ();
    FileOutputStream fos = null;
    try {
        fos = FileUtils.openOutputStream (destination);
        for (ChunkDownload chunk : chunks) {
            String filePath = chunk.getChunkFilePath ();
            InputStream ins = null;
            try {
                File chunkFile = new File (filePath);
                ins = FileUtils.openInputStream (chunkFile);
                IOUtils.copy (ins, fos);
                chunkFile.delete ();
            } catch (IOException e) {
                e.printStackTrace ();
            } finally {
                ins.close ();
            }
        }
        download.getWorkDir ().delete ();
        download.complete ();
    } catch (IOException e) {
        logger.error (""IO Exception while copying the chunk "" + e.getMessage (), e);
        e.printStackTrace ();
        throw new BindingException (""IO Exception while copying the chunk "" + e.getMessage (), e);
    } finally {
        try {
            fos.close ();
        } catch (IOException e) {
            logger.error (""IO Exception while copying closing stream of the target file "" + e.getMessage (), e);
            e.printStackTrace ();
            throw new BindingException (""IO Exception while copying closing stream of the target file "" + e.getMessage (), e);
        }
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1936137,"public void preparaEscrita (DadosSeriais dados, String dir) throws BasicException {
    String idArquivo = dados.getIdColeta ().toString ();
    if (dados.getIdResumo () != null) {
        idArquivo += ""_"" + dados.getIdResumo ().toString ();
    }
    if (dir == null || dir.trim ().equals ("""")) {
        throw BasicException.errorHandling (""Diret�rio Imagem de Dados n�o foi definido."", ""msgErroNaoExisteDiretorioImagem"", new String [] {}, log);
    }
    try {
        fos = new FileOutputStream (new File (dir.trim (), ""pdump."" + idArquivo + "".data.xml.zip""));
    } catch (FileNotFoundException e) {
        throw BasicException.errorHandling (""Erro ao abrir arquivo de dados xml para escrita"", ""msgErroCriarArquivoDadosXML"", e, log);
    }
    zipOutputStream = new ZipOutputStream (fos);
    zipOutputStream.setLevel (Deflater.DEFAULT_COMPRESSION);
    try {
        zipOutputStream.putNextEntry (new ZipEntry (""pdump."" + idArquivo + "".data.xml""));
        xmlWriter = XMLOutputFactory.newInstance ().createXMLStreamWriter (zipOutputStream, ENCODING);
    } catch (Exception e) {
        throw BasicException.errorHandling (""Erro ao criar entrada em arquivo compactado"", ""msgErroCriarEntradaZipArquivoDadosXML"", e, log);
    }
    XMLStreamWriter osw = null;
    try {
        xmlWriter = XMLOutputFactory.newInstance ().createXMLStreamWriter (zipOutputStream, ENCODING);
    } catch (Exception e) {
        throw BasicException.errorHandling (""Erro ao criar entrada em arquivo compactado"", ""msgErroCriarEntradaZipArquivoDadosXML"", e, log);
    }
    SimpleDateFormat dateFormat = new SimpleDateFormat (""yyyy-MM-dd'T'HH:mm:ss"");
    if (dados.getTipos ().size () > 0) {
        tipos = new int [dados.getTipos ().size ()];
        for (int c = 0;
        c < dados.getTipos ().size (); c ++) {
            String tipo = dados.getTipos ().get (c);
            if (tipo.equals (LIT_INTEIRO)) {
                tipos [c] = INTEIRO;
            } else if (tipo.equals (LIT_DECIMAL)) {
                tipos [c] = DECIMAL;
            } else if (tipo.equals (LIT_DATA)) {
                tipos [c] = DATA;
            } else {
                tipos [c] = TEXTO;
            }

        }
    }
    try {
        xmlWriter.writeStartDocument (ENCODING, ""1.0"");
        xmlWriter.writeStartElement (""coleta"");
        xmlWriter.writeAttribute (""xmlns:xsi"", ""http://www.w3.org/2001/XMLSchema-instance"");
        xmlWriter.writeAttribute (""xsi:noNamespaceSchemaLocation"", ""http://www.pingifes.lcc.ufmg.br/dtd/pingifes_dados_seriais.xsd"");
        xmlWriter.writeStartElement (""id"");
        xmlWriter.writeCharacters (idArquivo);
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""data"");
        xmlWriter.writeCharacters (dateFormat.format (dados.getDataColeta ()));
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""sql"");
        xmlWriter.writeCData (dados.getSql ());
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""cabecalho"");
        for (int c = 0;
        c < dados.getCabecalho ().size (); c ++) {
            xmlWriter.writeStartElement (""nome"");
            xmlWriter.writeAttribute (""tipo"", dados.getTipos ().get (c));
            xmlWriter.writeCharacters (dados.getCabecalho ().get (c));
            xmlWriter.writeEndElement ();
        }
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""quantidade"");
        xmlWriter.writeCharacters ("""" + dados.getQuantidade ());
        xmlWriter.writeEndElement ();
        xmlWriter.writeStartElement (""dados"");
    } catch (XMLStreamException e) {
        throw BasicException.errorHandling (""Erro ao escrever dados em arquivo compactado"", ""msgErroEscreverArquivoDadosXML"", e, log);
    }
    calculadorHash = new CalculaHash ();
}
",19301681,"private static void processFiles (final File packDir, final File file, final ZipOutputStream out) throws IOException {
    if (file.isDirectory ()) {
        final ZipEntry e = new ZipEntry (ZipUtils.convertFileName (packDir, file) + ""/"");
        out.putNextEntry (e);
        out.closeEntry ();
        final File [] files = file.listFiles ();
        for (final File f : files) ZipUtils.processFiles (packDir, f, out);

    } else {
        final BufferedInputStream bis = new BufferedInputStream (new FileInputStream (file));
        final ZipEntry e = new ZipEntry (ZipUtils.convertFileName (packDir, file));
        final CRC32 crc = new CRC32 ();
        out.putNextEntry (e);
        final byte [] buf = new byte [4096];
        int len = 0;
        while ((len = bis.read (buf)) > 0) {
            out.write (buf, 0, len);
            crc.update (buf, 0, len);
        }
        e.setCrc (crc.getValue ());
        out.closeEntry ();
        bis.close ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
251963,"File createJar (File jar, String...entries) throws IOException {
    OutputStream out = new FileOutputStream (jar);
    try {
        JarOutputStream jos = new JarOutputStream (out);
        for (String e : entries) {
            jos.putNextEntry (new JarEntry (getPathForZipEntry (e)));
            jos.write (getBodyForEntry (e).getBytes ());
        }
        jos.close ();
    } finally {
        out.close ();
    }
    return jar;
}
",22491212,"public void writeBookOutput (ZipOutputStream outputStream, String cleanSGML) {
    boolean isCompressedOutput = false;
    if (outputStream != null) {
        isCompressedOutput = true;
    }
    try {
        FileWriter fw = new FileWriter (bookPath);
        if (isCompressedOutput) {
            if (witsInstance.getOutputType ().equals (""solbook"")) {
                SolBookWriter cWriter = new SolBookWriter (witsInstance, cleanSGML, props);
                ZipEntry entry = new ZipEntry (bookPath.getName ());
                try {
                    outputStream.putNextEntry (entry);
                    outputStream.write (cWriter.getPartialBookBody ().getBytes ());
                    outputStream.closeEntry ();
                } catch (IOException ex) {
                    ex.printStackTrace ();
                }
            }
            if (witsInstance.getOutputType ().equals (""docbook"")) {
                DocBookWriter cWriter = new DocBookWriter (cleanSGML, props);
                ZipEntry entry = new ZipEntry (bookPath.getName ());
                try {
                    outputStream.putNextEntry (entry);
                    outputStream.write (cWriter.getPartialBookBody ().getBytes ());
                    outputStream.closeEntry ();
                } catch (IOException ex) {
                    ex.printStackTrace ();
                }
            }
        } else {
            if (witsInstance.getOutputType ().equals (""solbook"")) {
                SolBookWriter bWriter = new SolBookWriter (witsInstance, cleanSGML, props);
                fw.write (bWriter.getPartialBookBody ());
                fw.flush ();
                fw.close ();
            }
            if (witsInstance.getOutputType ().equals (""docbook"")) {
                DocBookWriter bWriter = new DocBookWriter (cleanSGML, props);
                fw.write (bWriter.getPartialBookBody ());
                fw.flush ();
                fw.close ();
            }
        }
    } catch (IOException e) {
        System.out.println (""Error while writing to: "" + bookPath + "". PLease check the path/permission."");
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
586503,"private static void readAndRewrite (File inFile, File outFile) throws IOException {
    ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile)));
    DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis);
    Dataset ds = DcmObjectFactory.getInstance ().newDataset ();
    dcmParser.setDcmHandler (ds.getDcmHandler ());
    dcmParser.parseDcmFile (null, Tags.PixelData);
    PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    System.out.println (""reading "" + inFile + ""..."");
    pdReader.readPixelData (false);
    ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile)));
    DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE;
    ds.writeDataset (out, dcmEncParam);
    ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ());
    System.out.println (""writing "" + outFile + ""..."");
    PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    pdWriter.writePixelData ();
    out.flush ();
    out.close ();
    System.out.println (""done!"");
}
",11965514,"private void checkRoundtrip (byte [] content) throws Exception {
    InputStream in = new ByteArrayInputStream (content);
    ByteArrayOutputStream out = new ByteArrayOutputStream ();
    CodecUtil.encodeQuotedPrintable (in, out);
    in = new QuotedPrintableInputStream (new ByteArrayInputStream (out.toByteArray ()));
    out = new ByteArrayOutputStream ();
    IOUtils.copy (in, out);
    assertEquals (content, out.toByteArray ());
}
",Copy File,Type-3 (WT3/4),TRUE
7158123,"public void truncateLog (long finalZxid) throws IOException {
    long highestZxid = 0;
    for (File f : dataDir.listFiles ()) {
        long zxid = isValidSnapshot (f);
        if (zxid == - 1) {
            LOG.warn (""Skipping "" + f);
            continue;
        }
        if (zxid > highestZxid) {
            highestZxid = zxid;
        }
    }
    File [] files = getLogFiles (dataLogDir.listFiles (), highestZxid);
    boolean truncated = false;
    for (File f : files) {
        FileInputStream fin = new FileInputStream (f);
        InputArchive ia = BinaryInputArchive.getArchive (fin);
        FileChannel fchan = fin.getChannel ();
        try {
            while (true) {
                byte [] bytes = ia.readBuffer (""txtEntry"");
                if (bytes.length == 0) {
                    throw new EOFException ();
                }
                InputArchive iab = BinaryInputArchive.getArchive (new ByteArrayInputStream (bytes));
                TxnHeader hdr = new TxnHeader ();
                deserializeTxn (iab, hdr);
                if (ia.readByte (""EOF"") != 'B') {
                    throw new EOFException ();
                }
                if (hdr.getZxid () == finalZxid) {
                    long pos = fchan.position ();
                    fin.close ();
                    FileOutputStream fout = new FileOutputStream (f);
                    FileChannel fchanOut = fout.getChannel ();
                    fchanOut.truncate (pos);
                    truncated = true;
                    break;
                }
            }
        } catch (EOFException eof) {
        }
        if (truncated == true) {
            break;
        }
    }
    if (truncated == false) {
        LOG.error (""Not able to truncate the log "" + Long.toHexString (finalZxid));
        System.exit (13);
    }
}
",8219190,"public static String stringOfUrl (String addr) throws IOException {
    ByteArrayOutputStream output = new ByteArrayOutputStream ();
    URL url = new URL (addr);
    IOUtils.copy (url.openStream (), output);
    return output.toString ();
}
",Copy File,Type-3 (WT3/4),TRUE
21247844,"public static void kopirujSoubor (File vstup, File vystup) throws IOException {
    FileChannel sourceChannel = new FileInputStream (vstup).getChannel ();
    FileChannel destinationChannel = new FileOutputStream (vystup).getChannel ();
    sourceChannel.transferTo (0, sourceChannel.size (), destinationChannel);
    sourceChannel.close ();
    destinationChannel.close ();
}
",23403205,"public void copyFile (File sourceFile, String toDir, boolean create, boolean overwrite) throws FileNotFoundException, IOException {
    FileInputStream source = null;
    FileOutputStream destination = null;
    byte [] buffer;
    int bytes_read;
    File toFile = new File (toDir);
    if (create && ! toFile.exists ()) toFile.mkdirs ();

    if (toFile.exists ()) {
        File destFile = new File (toDir + ""/"" + sourceFile.getName ());
        try {
            if (! destFile.exists () || overwrite) {
                source = new FileInputStream (sourceFile);
                destination = new FileOutputStream (destFile);
                buffer = new byte [1024];
                while (true) {
                    bytes_read = source.read (buffer);
                    if (bytes_read == - 1) break;

                    destination.write (buffer, 0, bytes_read);
                }
            }
        } catch (Exception exx) {
            exx.printStackTrace ();
        } finally {
            if (source != null) try {
                source.close ();
            } catch (IOException e) {
            }

            if (destination != null) try {
                destination.close ();
            } catch (IOException e) {
            }

        }
    }
}
",Copy File,Type-3 (WT3/4),TRUE
2706738,"public void takeScreenshot (String title) throws Exception {
    Calendar cal = Calendar.getInstance ();
    SimpleDateFormat sdf = new SimpleDateFormat (""yyyy_MM_dd_HH_mm_ss"");
    String time = sdf.format (cal.getTime ());
    Dimension screenSize = Toolkit.getDefaultToolkit ().getScreenSize ();
    Rectangle screenRectangle = new Rectangle (screenSize);
    Robot robot = new Robot ();
    BufferedImage image = robot.createScreenCapture (screenRectangle);
    File f = new File (report.getCurrentTestFolder (), ""screenshot_"" + time + "".png"");
    f.createNewFile ();
    ImageIO.write (image, ""png"", f);
    report.addLink (getTitle (""Screenshot""), ""file:///"" + f.getAbsolutePath ());
}
",13153590,"public void screenCapture () throws Exception {
    BufferedImage screencapture = new Robot ().createScreenCapture (new Rectangle (Toolkit.getDefaultToolkit ().getScreenSize ()));
    File file = new File (report.getCurrentTestFolder (), ""screencapture.jpg"");
    ImageIO.write (screencapture, ""jpg"", file);
    report.addLink (""screen capture"", ""screencapture.jpg"");
}
",Take Screenshot to File,Type-3 (WT3/4),TRUE
1956491,"public String setCrc32 () {
    CRC32 crc = new CRC32 ();
    crc.update (file);
    crc32 = """" + crc.getValue ();
    return crc32;
}
",19301681,"private static void processFiles (final File packDir, final File file, final ZipOutputStream out) throws IOException {
    if (file.isDirectory ()) {
        final ZipEntry e = new ZipEntry (ZipUtils.convertFileName (packDir, file) + ""/"");
        out.putNextEntry (e);
        out.closeEntry ();
        final File [] files = file.listFiles ();
        for (final File f : files) ZipUtils.processFiles (packDir, f, out);

    } else {
        final BufferedInputStream bis = new BufferedInputStream (new FileInputStream (file));
        final ZipEntry e = new ZipEntry (ZipUtils.convertFileName (packDir, file));
        final CRC32 crc = new CRC32 ();
        out.putNextEntry (e);
        final byte [] buf = new byte [4096];
        int len = 0;
        while ((len = bis.read (buf)) > 0) {
            out.write (buf, 0, len);
            crc.update (buf, 0, len);
        }
        e.setCrc (crc.getValue ());
        out.closeEntry ();
        bis.close ();
    }
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
1831903,"public static void buildKMZ (File kmzFile, Layer layer) throws Exception {
    if (! (layer instanceof TimeLoopGroundOverlay) && ! (layer instanceof GroundOverlayLayer)) throw new IOException (""Invalid layer type:"" + layer.getClass ().getName ());

    ZipOutputStream out = new ZipOutputStream (new FileOutputStream (kmzFile));
    String kmlDoc;
    if (layer instanceof TimeLoopGroundOverlay) {
        final TimeLoopGroundOverlay loop = (TimeLoopGroundOverlay) layer;
        kmlDoc = loop.toKML (false, true);
        for (GroundOverlayLayer ov : loop.getOverlays ()) {
            File f = ov.getFileFromCache ();
            String fName = f.getName ();
            logger.debug (""Adding Time Loop Ov to KMZ:"" + fName);
            out.putNextEntry (new ZipEntry (fName));
            out.write (Messages.readFile (f));
        }
        if (loop.getLegend () != null) {
            try {
                File f = loop.getLegend ().getFile ();
                logger.debug (""Adding Time Loop LEGEND to KMZ:"" + f.getName ());
                out.putNextEntry (new ZipEntry (f.getName ()));
                out.write (Messages.readFile (f));
            } catch (Exception e) {
                logger.error (""Error adding legend "" + loop.getLegend () + "" to kmz."" + e);
            }
        }
    } else {
        final GroundOverlayLayer gov = (GroundOverlayLayer) layer;
        kmlDoc = gov.toKML (false, false);
        File f = new File (gov.getTextureURL ().toURI ());
        String fName = f.getName ();
        logger.debug (""Adding Ground Overlay to KMZ:"" + fName);
        out.putNextEntry (new ZipEntry (fName));
        out.write (Messages.readFile (f));
    }
    out.putNextEntry (new ZipEntry (""doc.kml""));
    out.write (kmlDoc.getBytes ());
    out.close ();
}
",11464122,"public void addStringEntry (String filename, String data) throws Exception {
    zOut.putNextEntry (new ZipEntry (filename));
    zOut.write (data.getBytes ());
    zOut.closeEntry ();
    fileCount ++;
}
",Zip Files,Type-3 (WT3/4),FALSE
8434526,"private ZipOutputStream copyOOXMLContent (String signatureZipEntryName, OutputStream signedOOXMLOutputStream) throws IOException, ParserConfigurationException, SAXException, TransformerConfigurationException, TransformerFactoryConfigurationError, TransformerException {
    ZipOutputStream zipOutputStream = new ZipOutputStream (signedOOXMLOutputStream);
    ZipInputStream zipInputStream = new ZipInputStream (this.getOfficeOpenXMLDocumentURL ().openStream ());
    ZipEntry zipEntry;
    boolean hasOriginSigsRels = false;
    while (null != (zipEntry = zipInputStream.getNextEntry ())) {
        LOG.debug (""copy ZIP entry: "" + zipEntry.getName ());
        ZipEntry newZipEntry = new ZipEntry (zipEntry.getName ());
        zipOutputStream.putNextEntry (newZipEntry);
        if (""[Content_Types].xml"".equals (zipEntry.getName ())) {
            Document contentTypesDocument = loadDocumentNoClose (zipInputStream);
            Element typesElement = contentTypesDocument.getDocumentElement ();
            Element overrideElement = contentTypesDocument.createElementNS (""http://schemas.openxmlformats.org/package/2006/content-types"", ""Override"");
            overrideElement.setAttribute (""PartName"", ""/"" + signatureZipEntryName);
            overrideElement.setAttribute (""ContentType"", ""application/vnd.openxmlformats-package.digital-signature-xmlsignature+xml"");
            typesElement.appendChild (overrideElement);
            Element nsElement = contentTypesDocument.createElement (""ns"");
            nsElement.setAttributeNS (Constants.NamespaceSpecNS, ""xmlns:tns"", ""http://schemas.openxmlformats.org/package/2006/content-types"");
            NodeList nodeList = XPathAPI.selectNodeList (contentTypesDocument, ""/tns:Types/tns:Default[@Extension='sigs']"", nsElement);
            if (0 == nodeList.getLength ()) {
                Element defaultElement = contentTypesDocument.createElementNS (""http://schemas.openxmlformats.org/package/2006/content-types"", ""Default"");
                defaultElement.setAttribute (""Extension"", ""sigs"");
                defaultElement.setAttribute (""ContentType"", ""application/vnd.openxmlformats-package.digital-signature-origin"");
                typesElement.appendChild (defaultElement);
            }
            writeDocumentNoClosing (contentTypesDocument, zipOutputStream, false);
        } else if (""_rels/.rels"".equals (zipEntry.getName ())) {
            Document relsDocument = loadDocumentNoClose (zipInputStream);
            Element nsElement = relsDocument.createElement (""ns"");
            nsElement.setAttributeNS (Constants.NamespaceSpecNS, ""xmlns:tns"", ""http://schemas.openxmlformats.org/package/2006/relationships"");
            NodeList nodeList = XPathAPI.selectNodeList (relsDocument, ""/tns:Relationships/tns:Relationship[@Target='_xmlsignatures/origin.sigs']"", nsElement);
            if (0 == nodeList.getLength ()) {
                Element relationshipElement = relsDocument.createElementNS (""http://schemas.openxmlformats.org/package/2006/relationships"", ""Relationship"");
                relationshipElement.setAttribute (""Id"", ""rel-id-"" + UUID.randomUUID ().toString ());
                relationshipElement.setAttribute (""Type"", ""http://schemas.openxmlformats.org/package/2006/relationships/digital-signature/origin"");
                relationshipElement.setAttribute (""Target"", ""_xmlsignatures/origin.sigs"");
                relsDocument.getDocumentElement ().appendChild (relationshipElement);
            }
            writeDocumentNoClosing (relsDocument, zipOutputStream, false);
        } else if (""_xmlsignatures/_rels/origin.sigs.rels"".equals (zipEntry.getName ())) {
            hasOriginSigsRels = true;
            Document originSignRelsDocument = loadDocumentNoClose (zipInputStream);
            Element relationshipElement = originSignRelsDocument.createElementNS (""http://schemas.openxmlformats.org/package/2006/relationships"", ""Relationship"");
            String relationshipId = ""rel-"" + UUID.randomUUID ().toString ();
            relationshipElement.setAttribute (""Id"", relationshipId);
            relationshipElement.setAttribute (""Type"", ""http://schemas.openxmlformats.org/package/2006/relationships/digital-signature/signature"");
            String target = FilenameUtils.getName (signatureZipEntryName);
            LOG.debug (""target: "" + target);
            relationshipElement.setAttribute (""Target"", target);
            originSignRelsDocument.getDocumentElement ().appendChild (relationshipElement);
            writeDocumentNoClosing (originSignRelsDocument, zipOutputStream, false);
        } else {
            IOUtils.copy (zipInputStream, zipOutputStream);
        }

    }
    if (false == hasOriginSigsRels) {
        addOriginSigsRels (signatureZipEntryName, zipOutputStream);
        addOriginSigs (zipOutputStream);
    }
    zipInputStream.close ();
    return zipOutputStream;
}
",11370967,"public void copyFile (File in, File out) throws Exception {
    FileChannel ic = new FileInputStream (in).getChannel ();
    FileChannel oc = new FileOutputStream (out).getChannel ();
    ic.transferTo (0, ic.size (), oc);
    ic.close ();
    oc.close ();
}
",Copy File,Type-3 (WT3/4),TRUE
1747657,"private void addFileToZip (String filename, ZipOutputStream out) throws IOException {
    out.putNextEntry (new ZipEntry (filename));
    out.closeEntry ();
}
",4698218,"public static void zi (String s, String z, int i) throws Exception {
    byte [] buffer = s.getBytes (""UTF-8"");
    ZipOutputStream out = new ZipOutputStream (new FileOutputStream (z + "".zip""));
    out.putNextEntry (new ZipEntry (i + "".txt""));
    out.write (buffer);
    out.closeEntry ();
    out.close ();
    System.out.println (i + "".txt -> "" + z + "".zip"");
}
",Zip Files,Type-3 (WT3/4),FALSE
161298,"private void saveZipEntries (Object [] entries, ZipOutputStream zos) throws IOException {
    for (int i = 0;
    i < entries.length;) {
        String entryName = (String) entries [i ++];
        Object entry = entries [i ++];
        zos.putNextEntry (new ZipEntry (entryName));
        if (entry instanceof String) {
            this.saveContents ((String) entry, zos);
        } else {
            this.saveZipEntries ((Object []) entry, zos);
        }
    }
}
",9781386,"public void run () {
    root.setCursor (Cursor.getPredefinedCursor (3));
    try {
        tempArchiveFile = File.createTempFile (""JZip"", "".zip"");
        if (table.getRowCount () != delRows.length) {
            stream = new FileOutputStream (tempArchiveFile);
            out = new ZipOutputStream (stream);
            boolean aflag [] = new boolean [table.getRowCount ()];
            for (int i = 0;
            i < table.getRowCount (); i ++) {
                aflag [i] = false;
            }
            for (int j = 0;
            j < delRows.length; j ++) {
                aflag [delRows [j]] = true;
            }
            ZipFile zipfile = new ZipFile (archiveFile);
            for (int k = 0;
            k < table.getRowCount (); k ++) {
                if (! aflag [k]) {
                    Object obj = ziptm.getRealValueAt (k, 6);
                    String s1 = ziptm.getRealValueAt (k, 0).toString ();
                    String s2 = s1;
                    String s3 = """";
                    if (obj != null) {
                        String s4 = obj.toString ();
                        s2 = s4 + s1;
                    }
                    ZipEntry zipentry = zipfile.getEntry (s2.replace (File.separatorChar, '/'));
                    if (zipentry == null) {
                        System.out.println (""The entry with name<"" + s2 + ""> is null"");
                    } else {
                        InputStream inputstream = zipfile.getInputStream (zipentry);
                        out.putNextEntry (zipentry);
                        do {
                            int l = inputstream.read (buffer, 0, buffer.length);
                            if (l <= 0) {
                                break;
                            }
                            out.write (buffer, 0, l);
                        } while (true);
                        inputstream.close ();
                        out.closeEntry ();
                    }
                }
            }
            zipfile.close ();
            out.close ();
            stream.close ();
        }
        String s = archiveFile.getAbsolutePath ();
        archiveFile.delete ();
        tempArchiveFile.renameTo (new File (s));
        tempArchiveFile.getCanonicalPath ();
        openArchive (new File (s));
        table.clearSelection ();
        setStatus (""Totally "" + delRows.length + "" file(s) deleted from this archive!"");
    } catch (Exception exception) {
        exception.printStackTrace ();
        setStatus (""Error: "" + exception.getMessage ());
    }
    root.setCursor (Cursor.getPredefinedCursor (0));
    notifyAll ();
}
",Zip Files,Type-3 (WT3/4),FALSE
1093295,"private static void createZip (final File destinationFile, final List < File > files, final int cutFileNameIndex) throws IOException {
    final ZipOutputStream oStream = new ZipOutputStream (new FileOutputStream (destinationFile));
    for (final File file : files) {
        final String fullFileName = file.getAbsolutePath ();
        final String cuttedFileName = fullFileName.substring (cutFileNameIndex);
        final String osIndependendFileName = cuttedFileName.replace (File.separatorChar, '/');
        oStream.putNextEntry (new ZipEntry (osIndependendFileName));
        final FileInputStream iStream = new FileInputStream (file);
        FileOperations.copy (iStream, oStream);
        oStream.closeEntry ();
        iStream.close ();
    }
    oStream.close ();
}
",10042671,"public void addNonKMLFile (final byte [] file, final String inZipFilename) throws IOException {
    ZipEntry entry = new ZipEntry (inZipFilename);
    this.zipOut.putNextEntry (entry);
    this.zipOut.write (file);
    log.info (entry.getName () + "" added to kmz."");
}
",Zip Files,Type-3 (WT3/4),FALSE
5048822,"public static String md5 (String string) throws NoSuchAlgorithmException {
    MessageDigest md5 = MessageDigest.getInstance (""MD5"");
    md5.reset ();
    md5.update (string.getBytes ());
    byte [] result = md5.digest ();
    StringBuffer hexString = new StringBuffer ();
    for (int i = 0;
    i < result.length; i ++) {
        hexString.append (Integer.toHexString ((result [i] & 0xFF) | 0x100).toLowerCase ().substring (1, 3));
    }
    return hexString.toString ();
}
",8446876,"public static byte [] ComputeForBinary (String ThisString) throws Exception {
    byte [] Result;
    MessageDigest MD5Hasher;
    MD5Hasher = MessageDigest.getInstance (""MD5"");
    MD5Hasher.update (ThisString.getBytes (""iso-8859-1""));
    Result = MD5Hasher.digest ();
    return Result;
}
",Secure Hash,Type-3 (WT3/4),TRUE
6331499,"private OutputStream getOutputStream (boolean delete, long timeStamp) throws IOException {
    final String nestedURL = getNestedURL ();
    final File tempFile = File.createTempFile (""Archive"", ""zip"");
    InputStream sourceInputStream = null;
    OutputStream tempOutputStream = null;
    try {
        tempOutputStream = new FileOutputStream (tempFile);
        try {
            sourceInputStream = createInputStream (nestedURL);
        } catch (IOException exception) {
        }
        OutputStream outputStream = tempOutputStream;
        InputStream inputStream = sourceInputStream;
        int archiveSeparator = urlString.indexOf (nestedURL) + nestedURL.length ();
        int nextArchiveSeparator = urlString.indexOf (""!/"", archiveSeparator + 2);
        ZipOutputStream zipOutputStream;
        final byte [] bytes = new byte [4096];
        ZipEntry outputZipEntry;
        boolean found = false;
        for (;;) {
            String entry = URI.decode (nextArchiveSeparator < 0 ? urlString.substring (archiveSeparator + 2) : urlString.substring (archiveSeparator + 2, nextArchiveSeparator));
            zipOutputStream = null;
            ZipInputStream zipInputStream = inputStream == null ? null : new ZipInputStream (inputStream);
            inputStream = zipInputStream;
            while (zipInputStream != null && zipInputStream.available () >= 0) {
                ZipEntry zipEntry = zipInputStream.getNextEntry ();
                if (zipEntry == null) {
                    break;
                } else {
                    boolean match = entry.equals (zipEntry.getName ());
                    if (! found) {
                        found = match && nextArchiveSeparator < 0;
                    }
                    if (timeStamp != - 1 || ! match) {
                        if (zipOutputStream == null) {
                            zipOutputStream = new ZipOutputStream (outputStream);
                            outputStream = zipOutputStream;
                        }
                        if (timeStamp != - 1 && match && nextArchiveSeparator < 0) {
                            zipEntry.setTime (timeStamp);
                        }
                        zipOutputStream.putNextEntry (zipEntry);
                        for (int size;
                        (size = zipInputStream.read (bytes, 0, bytes.length)) > - 1;) {
                            zipOutputStream.write (bytes, 0, size);
                        }
                    }
                }
            }
            archiveSeparator = nextArchiveSeparator;
            nextArchiveSeparator = urlString.indexOf (""!/"", archiveSeparator + 2);
            if ((delete || timeStamp != - 1) && archiveSeparator < 0) {
                if (! found) {
                    throw new IOException (""Archive entry not found "" + urlString);
                }
                outputZipEntry = null;
                break;
            } else {
                outputZipEntry = new ZipEntry (entry);
                if (zipOutputStream == null) {
                    zipOutputStream = new ZipOutputStream (outputStream);
                    outputStream = zipOutputStream;
                }
                zipOutputStream.putNextEntry (outputZipEntry);
                if (archiveSeparator > 0) {
                    continue;
                } else {
                    break;
                }
            }
        }
        tempOutputStream = null;
        final boolean deleteRequired = sourceInputStream != null;
        FilterOutputStream result = new FilterOutputStream (zipOutputStream == null ? outputStream : zipOutputStream) {
            protected boolean isClosed;
            @Override
            public void close () throws IOException {
                if (! isClosed) {
                    isClosed = true;
                    super.close ();
                    boolean useRenameTo = nestedURL.startsWith (""file:"");
                    if (useRenameTo) {
                        File targetFile = new File (URI.decode (nestedURL.substring (5)));
                        if (deleteRequired && ! targetFile.delete ()) {
                            throw new IOException (""cannot delete "" + targetFile.getPath ());
                        } else if (! tempFile.renameTo (targetFile)) {
                            useRenameTo = false;
                        }

                    }
                    if (! useRenameTo) {
                        InputStream inputStream = null;
                        OutputStream outputStream = null;
                        try {
                            inputStream = new FileInputStream (tempFile);
                            outputStream = createOutputStream (nestedURL);
                            for (int size;
                            (size = inputStream.read (bytes, 0, bytes.length)) > - 1;) {
                                outputStream.write (bytes, 0, size);
                            }
                        } finally {
                            if (inputStream != null) {
                                inputStream.close ();
                            }
                            if (outputStream != null) {
                                outputStream.close ();
                            }
                        }
                    }
                }
            }}

        ;
        return outputZipEntry == null ? result : yield (outputZipEntry, result);
    } finally {
        if (tempOutputStream != null) {
            tempOutputStream.close ();
        }
        if (sourceInputStream != null) {
            sourceInputStream.close ();
        }
    }
}
",15548515,"private void downloadZipDocument (HttpServletResponse response) throws Exception {
    ZipOutputStream out = new ZipOutputStream (response.getOutputStream ());
    out.setMethod (ZipOutputStream.DEFLATED);
    for (int i = 0;
    i < this.lstZipFileName.size (); i ++) {
        String documentName = (String) this.lstZipFileName.get (i);
        String documentPath = (String) this.lstZipFilePath.get (i);
        if (""NO_FILE"".equals (documentPath)) {
            out.putNextEntry (new ZipEntry (documentName));
        } else {
            out.putNextEntry (new ZipEntry (documentName));
            File file = new File (documentPath);
            if (file.exists ()) {
                FileInputStream in = new FileInputStream (file);
                byte [] buffer = new byte [8192];
                int length = - 1;
                while ((length = in.read (buffer, 0, 8192)) != - 1) {
                    out.write (buffer, 0, length);
                }
                in.close ();
            }
        }
    }
    out.flush ();
    out.close ();
}
",Zip Files,Type-3 (WT3/4),TRUE
751335,"private static void readAndRewrite (File inFile, File outFile) throws IOException {
    ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile)));
    DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis);
    Dataset ds = DcmObjectFactory.getInstance ().newDataset ();
    dcmParser.setDcmHandler (ds.getDcmHandler ());
    dcmParser.parseDcmFile (null, Tags.PixelData);
    PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    System.out.println (""reading "" + inFile + ""..."");
    pdReader.readPixelData (false);
    ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile)));
    DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE;
    ds.writeDataset (out, dcmEncParam);
    ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ());
    System.out.println (""writing "" + outFile + ""..."");
    PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    pdWriter.writePixelData ();
    out.flush ();
    out.close ();
    System.out.println (""done!"");
}
",14058237,"public boolean renameTo (File dest) throws IOException {
    if (dest == null) {
        throw new NullPointerException (""dest"");
    }
    if (! file.renameTo (dest)) {
        FileInputStream inputStream = new FileInputStream (file);
        FileOutputStream outputStream = new FileOutputStream (dest);
        FileChannel in = inputStream.getChannel ();
        FileChannel out = outputStream.getChannel ();
        long destsize = in.transferTo (0, size, out);
        in.close ();
        out.close ();
        if (destsize == size) {
            file.delete ();
            file = dest;
            isRenamed = true;
            return true;
        } else {
            dest.delete ();
            return false;
        }
    }
    file = dest;
    isRenamed = true;
    return true;
}
",Copy File,Type-3 (WT3/4),TRUE
4016687,"public static void main (String [] args) {
    FTPClient client = new FTPClient ();
    String sFTP = ""ftp.miservidor.com"";
    String sUser = ""usuario"";
    String sPassword = ""password"";
    try {
        System.out.println (""Conectandose a "" + sFTP);
        client.connect (sFTP);
        boolean login = client.login (sUser, sPassword);
        if (login) {
            System.out.println (""Login correcto"");
            boolean logout = client.logout ();
            if (logout) {
                System.out.println (""Logout del servidor FTP"");
            }
        } else {
            System.out.println (""Error en el login."");
        }
        System.out.println (""Desconectando."");
        client.disconnect ();
    } catch (IOException ioe) {
        ioe.printStackTrace ();
    }
}
",16095007,"private static void getFileFtp (String user, String password, String host, int port, String fileName, String location) throws Exception {
    Log.info (""\nretrieve "" + fileName + NEW_LINE);
    FTPClient client = new FTPClient ();
    client.connect (host, port);
    int reply = client.getReplyCode ();
    if (! FTPReply.isPositiveCompletion (reply)) {
        throw new Exception (""FTP fail to connect"");
    }
    if (! client.login (user, password)) {
        throw new Exception (""FTP fail to login"");
    }
    try {
        File locationFile = new File (location);
        File dest = new File (locationFile, fileName);
        if (dest.exists ()) {
            dest.delete ();
        } else {
            locationFile.mkdirs ();
        }
        boolean status = client.changeWorkingDirectory (""/"");
        Log.info (""chdir-status:"" + status + NEW_LINE);
        client.setFileTransferMode (FTPClient.BINARY_FILE_TYPE);
        client.setFileType (FTPClient.BINARY_FILE_TYPE);
        client.enterLocalActiveMode ();
        InputStream in = client.retrieveFileStream (fileName);
        if (in == null) {
            Log.error (""Input stream is null\n"");
            throw new Exception (""Fail to retrieve file "" + fileName);
        }
        Thread.sleep (3000);
        saveInputStreamToFile (in, new File (location, fileName));
    } finally {
        client.disconnect ();
    }
}
",Connect to FTP Server,Type-3 (WT3/4),TRUE
6085930,"public void update () {
    if (! updatable) {
        Main.fenetre ().erreur (Fenetre.OLD_VERSION);
        return;
    }
    try {
        Main.fenetre ().update ();
        Element remoteRoot = new SAXBuilder ().build (xml).getRootElement ();
        addPackages = new HashMap < Integer, PackageVersion > ();
        Iterator < ? > iterElem = remoteRoot.getChildren ().iterator ();
        while (iterElem.hasNext ()) {
            PackageVersion pack = new PackageVersion ((Element) iterElem.next ());
            addPackages.put (pack.id (), pack);
        }
        removePackages = new HashMap < Integer, PackageVersion > ();
        iterElem = root.getChildren (""package"").iterator ();
        while (iterElem.hasNext ()) {
            PackageVersion pack = new PackageVersion ((Element) iterElem.next ());
            int id = pack.id ();
            if (! addPackages.containsKey (id)) {
                removePackages.put (id, pack);
            } else if (addPackages.get (id).version ().equals (pack.version ())) {
                addPackages.remove (id);
            } else {
                addPackages.get (id).ecrase ();
            }

        }
        Iterator < PackageVersion > iterPack = addPackages.values ().iterator ();
        while (iterPack.hasNext ()) {
            install (iterPack.next ());
        }
        iterPack = removePackages.values ().iterator ();
        while (iterPack.hasNext ()) {
            remove (iterPack.next ());
        }
        if (offline) {
            Runtime.getRuntime ().addShutdownHook (new AddPackage (xml, ""versions.xml""));
            Main.fenetre ().erreur (Fenetre.UPDATE_TERMINE_RESTART);
        } else {
            File oldXML = new File (""versions.xml"");
            oldXML.delete ();
            oldXML.createNewFile ();
            FileChannel out = new FileOutputStream (oldXML).getChannel ();
            FileChannel in = new FileInputStream (xml).getChannel ();
            in.transferTo (0, in.size (), out);
            in.close ();
            out.close ();
            xml.delete ();
            if (restart) {
                Main.fenetre ().erreur (Fenetre.UPDATE_TERMINE_RESTART);
            } else {
                Main.updateVersion ();
            }
        }
    } catch (Exception e) {
        Main.fenetre ().erreur (Fenetre.ERREUR_UPDATE, e);
    }
}
",8788332,"private void printToStdout (InputStream in) throws IOException {
    try {
        IOUtils.copyBytes (in, System.out, getConf (), false);
    } finally {
        in.close ();
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1686152,"public void setUp () throws IOException {
    tmp = TestingUtil.tmpFile (new File ("".""));
    ZipOutputStream os = new ZipOutputStream (new FileOutputStream (tmp));
    os.putNextEntry (new ZipEntry (""key0""));
    os.write (0x01);
    os.write (0x05);
    os.closeEntry ();
    os.putNextEntry (new ZipEntry (""key1""));
    os.write (0x02);
    os.closeEntry ();
    os.putNextEntry (new ZipEntry (""properties""));
    os.write (""foo=bar\n"".getBytes ());
    os.closeEntry ();
    os.close ();
    storer = new ZipStorer (new ZipFile (tmp));
}
",8746579,"public Boolean execute (String sDestinationFilename) {
    ResourcesManager manager = new ResourcesManager ();
    BufferedInputStream oOrigin = null;
    FileOutputStream oDestination;
    ZipOutputStream oOutput;
    byte [] aData;
    try {
        System.out.println (""Compressing the model"");
        oDestination = new FileOutputStream (sDestinationFilename);
        oOutput = new ZipOutputStream (new BufferedOutputStream (oDestination));
        Collection < File > files = manager.getFiles (tempFilePath);
        aData = new byte [BUFFER_SIZE];
        Iterator < File > fileIterator = files.iterator ();
        while (fileIterator.hasNext ()) {
            File currentFile = fileIterator.next ();
            String sFilename = currentFile.getAbsolutePath ();
            sFilename = LibraryString.replaceAll (sFilename, Strings.BAR135, Strings.BAR45);
            FileInputStream fisInput = new FileInputStream (sFilename);
            oOrigin = new BufferedInputStream (fisInput, BUFFER_SIZE);
            sFilename = sFilename.substring (sFilename.indexOf (tempFilePath) + tempFilePath.length () + 1);
            ZipEntry oEntry = new ZipEntry (sFilename.replace ('\\', '/'));
            oOutput.putNextEntry (oEntry);
            int iCount;
            while ((iCount = oOrigin.read (aData, 0, BUFFER_SIZE)) != - 1) {
                oOutput.write (aData, 0, iCount);
            }
            oOrigin.close ();
            fisInput.close ();
        }
        oOutput.close ();
        System.out.println (""Model compressed"");
        AgentFilesystem.removeDir (tempFilePath);
    } catch (Exception oException) {
        oException.printStackTrace ();
        return false;
    }
    return true;
}
",Zip Files,Type-3 (WT3/4),FALSE
12542684,"public ServiceAdapterIfc deploy (String session, String name, byte jarBytes [], String jarName, String serviceClass, String serviceInterface) throws RemoteException, MalformedURLException, StartServiceException, SessionException {
    try {
        File jarFile = new File (jarName);
        jarName = jarFile.getName ();
        String jarName2 = jarName;
        jarFile = new File (jarName2);
        int n = 0;
        while (jarFile.exists ()) {
            jarName2 = jarName + n ++;
            jarFile = new File (jarName2);
        }
        FileOutputStream fos = new FileOutputStream (jarName2);
        IOUtils.copy (new ByteArrayInputStream (jarBytes), fos);
        SCClassLoader cl = new SCClassLoader (new URL [] {new URL (""file://"" + jarFile.getAbsolutePath ())}, getMasterNode ().getSCClassLoaderCounter ());
        return startService (session, name, serviceClass, serviceInterface, cl);
    } catch (SessionException e) {
        throw e;
    } catch (Exception e) {
        throw new StartServiceException (""Could not deploy service: "" + e.getMessage (), e);
    }
}
",17551920,"@Override
public void execute () throws ProcessorExecutionException {
    try {
        if (getSource ().getPaths () == null || getSource ().getPaths ().size () == 0 || getDestination ().getPaths () == null || getDestination ().getPaths ().size () == 0) {
            throw new ProcessorExecutionException (""No input and/or output paths specified."");
        }
        String temp_dir_prefix = getDestination ().getPath ().getParent ().toString () + ""/bcc_"" + getDestination ().getPath ().getName () + ""_"";
        SequenceTempDirMgr dirMgr = new SequenceTempDirMgr (temp_dir_prefix, context);
        dirMgr.setSeqNum (0);
        Path tmpDir;
        System.out.println (""++++++>"" + dirMgr.getSeqNum () + "": Transform input to AdjSetVertex"");
        Transformer transformer = new OutAdjVertex2AdjSetVertexTransformer ();
        transformer.setConf (context);
        transformer.setSrcPath (getSource ().getPath ());
        tmpDir = dirMgr.getTempDir ();
        transformer.setDestPath (tmpDir);
        transformer.setMapperNum (getMapperNum ());
        transformer.setReducerNum (getReducerNum ());
        transformer.execute ();
        System.out.println (""++++++>"" + dirMgr.getSeqNum () + "": Transform input to LabeledAdjSetVertex"");
        Vertex2LabeledTransformer l_transformer = new Vertex2LabeledTransformer ();
        l_transformer.setConf (context);
        l_transformer.setSrcPath (tmpDir);
        tmpDir = dirMgr.getTempDir ();
        l_transformer.setDestPath (tmpDir);
        l_transformer.setMapperNum (getMapperNum ());
        l_transformer.setReducerNum (getReducerNum ());
        l_transformer.setOutputValueClass (LabeledAdjSetVertex.class);
        l_transformer.execute ();
        Graph src;
        Graph dest;
        Path path_to_remember = tmpDir;
        System.out.println (""++++++>"" + dirMgr.getSeqNum () + "": SpanningTreeRootChoose"");
        src = new Graph (Graph.defaultGraph ());
        src.setPath (tmpDir);
        dest = new Graph (Graph.defaultGraph ());
        tmpDir = dirMgr.getTempDir ();
        dest.setPath (tmpDir);
        GraphAlgorithm choose_root = new SpanningTreeRootChoose ();
        choose_root.setConf (context);
        choose_root.setSource (src);
        choose_root.setDestination (dest);
        choose_root.setMapperNum (getMapperNum ());
        choose_root.setReducerNum (getReducerNum ());
        choose_root.execute ();
        Path the_file = new Path (tmpDir.toString () + ""/part-00000"");
        FileSystem client = FileSystem.get (context);
        if (! client.exists (the_file)) {
            throw new ProcessorExecutionException (""Did not find the chosen vertex in "" + the_file.toString ());
        }
        FSDataInputStream input_stream = client.open (the_file);
        ByteArrayOutputStream output_stream = new ByteArrayOutputStream ();
        IOUtils.copyBytes (input_stream, output_stream, context, false);
        String the_line = output_stream.toString ();
        String root_vertex_id = the_line.substring (SpanningTreeRootChoose.SPANNING_TREE_ROOT.length ()).trim ();
        input_stream.close ();
        output_stream.close ();
        System.out.println (""++++++> Chosen the root of spanning tree = "" + root_vertex_id);
        while (true) {
            System.out.println (""++++++>"" + dirMgr.getSeqNum () + "" Generate the spanning tree rooted at : ("" + root_vertex_id + "") from "" + tmpDir);
            src = new Graph (Graph.defaultGraph ());
            src.setPath (path_to_remember);
            tmpDir = dirMgr.getTempDir ();
            dest = new Graph (Graph.defaultGraph ());
            dest.setPath (tmpDir);
            path_to_remember = tmpDir;
            GraphAlgorithm spanning = new SpanningTreeGenerate ();
            spanning.setConf (context);
            spanning.setSource (src);
            spanning.setDestination (dest);
            spanning.setMapperNum (getMapperNum ());
            spanning.setReducerNum (getReducerNum ());
            spanning.setParameter (ConstantLabels.ROOT_ID, root_vertex_id);
            spanning.execute ();
            System.out.println (""++++++>"" + dirMgr.getSeqNum () + "" Test spanning convergence"");
            src = new Graph (Graph.defaultGraph ());
            src.setPath (tmpDir);
            tmpDir = dirMgr.getTempDir ();
            dest = new Graph (Graph.defaultGraph ());
            dest.setPath (tmpDir);
            GraphAlgorithm conv_tester = new SpanningConvergenceTest ();
            conv_tester.setConf (context);
            conv_tester.setSource (src);
            conv_tester.setDestination (dest);
            conv_tester.setMapperNum (getMapperNum ());
            conv_tester.setReducerNum (getReducerNum ());
            conv_tester.execute ();
            long vertexes_out_of_tree = MRConsoleReader.getMapOutputRecordNum (conv_tester.getFinalStatus ());
            System.out.println (""++++++> number of vertexes out of the spanning tree = "" + vertexes_out_of_tree);
            if (vertexes_out_of_tree == 0) {
                break;
            }
        }
        System.out.println (""++++++> From spanning tree to sets of edges"");
        src = new Graph (Graph.defaultGraph ());
        src.setPath (path_to_remember);
        tmpDir = dirMgr.getTempDir ();
        dest = new Graph (Graph.defaultGraph ());
        dest.setPath (tmpDir);
        GraphAlgorithm tree2set = new Tree2EdgeSet ();
        tree2set.setConf (context);
        tree2set.setSource (src);
        tree2set.setDestination (dest);
        tree2set.setMapperNum (getMapperNum ());
        tree2set.setReducerNum (getReducerNum ());
        tree2set.execute ();
        long map_input_records_num = - 1;
        long map_output_records_num = - 2;
        Stack < Path > expanding_stack = new Stack < Path > ();
        do {
            System.out.println (""++++++>"" + dirMgr.getSeqNum () + "": EdgeSetMinorJoin"");
            GraphAlgorithm minorjoin = new EdgeSetMinorJoin ();
            minorjoin.setConf (context);
            src = new Graph (Graph.defaultGraph ());
            src.setPath (tmpDir);
            dest = new Graph (Graph.defaultGraph ());
            tmpDir = dirMgr.getTempDir ();
            dest.setPath (tmpDir);
            minorjoin.setSource (src);
            minorjoin.setDestination (dest);
            minorjoin.setMapperNum (getMapperNum ());
            minorjoin.setReducerNum (getReducerNum ());
            minorjoin.execute ();
            expanding_stack.push (tmpDir);
            System.out.println (""++++++>"" + dirMgr.getSeqNum () + "": EdgeSetJoin"");
            GraphAlgorithm join = new EdgeSetJoin ();
            join.setConf (context);
            src = new Graph (Graph.defaultGraph ());
            src.setPath (tmpDir);
            dest = new Graph (Graph.defaultGraph ());
            tmpDir = dirMgr.getTempDir ();
            dest.setPath (tmpDir);
            join.setSource (src);
            join.setDestination (dest);
            join.setMapperNum (getMapperNum ());
            join.setReducerNum (getReducerNum ());
            join.execute ();
            map_input_records_num = MRConsoleReader.getMapInputRecordNum (join.getFinalStatus ());
            map_output_records_num = MRConsoleReader.getMapOutputRecordNum (join.getFinalStatus ());
            System.out.println (""++++++> map in/out : "" + map_input_records_num + ""/"" + map_output_records_num);
        } while (map_input_records_num != map_output_records_num);
        while (expanding_stack.size () > 0) {
            System.out.println (""++++++>"" + dirMgr.getSeqNum () + "": EdgeSetExpand"");
            GraphAlgorithm expand = new EdgeSetExpand ();
            expand.setConf (context);
            src = new Graph (Graph.defaultGraph ());
            src.addPath (expanding_stack.pop ());
            src.addPath (tmpDir);
            dest = new Graph (Graph.defaultGraph ());
            tmpDir = dirMgr.getTempDir ();
            dest.setPath (tmpDir);
            expand.setSource (src);
            expand.setDestination (dest);
            expand.setMapperNum (getMapperNum ());
            expand.setReducerNum (getReducerNum ());
            expand.execute ();
            System.out.println (""++++++>"" + dirMgr.getSeqNum () + "": EdgeSetMinorExpand"");
            GraphAlgorithm minorexpand = new EdgeSetMinorExpand ();
            minorexpand.setConf (context);
            src = new Graph (Graph.defaultGraph ());
            src.setPath (tmpDir);
            dest = new Graph (Graph.defaultGraph ());
            tmpDir = dirMgr.getTempDir ();
            dest.setPath (tmpDir);
            minorexpand.setSource (src);
            minorexpand.setDestination (dest);
            minorexpand.setMapperNum (getMapperNum ());
            minorexpand.setReducerNum (getReducerNum ());
            minorexpand.execute ();
        }
        System.out.println (""++++++>"" + dirMgr.getSeqNum () + "": EdgeSetSummarize"");
        GraphAlgorithm summarize = new EdgeSetSummarize ();
        summarize.setConf (context);
        src = new Graph (Graph.defaultGraph ());
        src.setPath (tmpDir);
        dest = new Graph (Graph.defaultGraph ());
        dest.setPath (getDestination ().getPath ());
        summarize.setSource (src);
        summarize.setDestination (dest);
        summarize.setMapperNum (getMapperNum ());
        summarize.setReducerNum (getReducerNum ());
        summarize.execute ();
        dirMgr.deleteAll ();
    } catch (IOException e) {
        throw new ProcessorExecutionException (e);
    } catch (IllegalAccessException e) {
        throw new ProcessorExecutionException (e);
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1820410,"public static void zipDirectory (String dir, String zipfile) throws IOException, IllegalArgumentException {
    File d = new File (dir);
    if (! d.isDirectory ()) throw new IllegalArgumentException (""Not a directory:  "" + dir);

    String [] entries = d.list ();
    byte [] buffer = new byte [4096];
    int bytesRead;
    ZipOutputStream out = new ZipOutputStream (new FileOutputStream (zipfile));
    for (int i = 0;
    i < entries.length; i ++) {
        File f = new File (d, entries [i]);
        if (f.isDirectory ()) continue;

        FileInputStream in = new FileInputStream (f);
        ZipEntry entry = new ZipEntry (f.getPath ());
        out.putNextEntry (entry);
        while ((bytesRead = in.read (buffer)) != - 1) out.write (buffer, 0, bytesRead);

        in.close ();
    }
    out.close ();
}
",6944635,"protected static void scaleImage (InputStream in, String name, ZipOutputStream out, double scaleX, double scaleY) throws Exception {
    BufferedImage img = ImageIO.read (in);
    Image scaled = img.getScaledInstance ((int) (img.getWidth () * scaleX), (int) (img.getHeight () * scaleY), Image.SCALE_SMOOTH);
    BufferedImage bScaled = new BufferedImage (img.getWidth (), img.getHeight (), BufferedImage.TYPE_INT_ARGB);
    bScaled.getGraphics ().drawImage (scaled, 0, 0, null);
    out.putNextEntry (new ZipEntry (name));
    ImageIO.write (bScaled, ""PNG"", out);
}
",Zip Files,Type-3 (WT3/4),FALSE
912653,"public static void main (String [] args) {
    if (args.length != 1) {
        System.out.println (""Usage: GUnzip source"");
        return;
    }
    String zipname, source;
    if (args [0].endsWith ("".gz"")) {
        zipname = args [0];
        source = args [0].substring (0, args [0].length () - 3);
    } else {
        zipname = args [0] + "".gz"";
        source = args [0];
    }
    GZIPInputStream zipin;
    try {
        FileInputStream in = new FileInputStream (zipname);
        zipin = new GZIPInputStream (in);
    } catch (IOException e) {
        System.out.println (""Couldn't open "" + zipname + ""."");
        return;
    }
    byte [] buffer = new byte [sChunk];
    try {
        FileOutputStream out = new FileOutputStream (source);
        int length;
        while ((length = zipin.read (buffer, 0, sChunk)) != - 1) out.write (buffer, 0, length);

        out.close ();
    } catch (IOException e) {
        System.out.println (""Couldn't decompress "" + args [0] + ""."");
    }
    try {
        zipin.close ();
    } catch (IOException e) {
    }
}
",13680335,"private String fetchCompareContent () throws IOException {
    URL url = new URL (compareTo);
    StringWriter sw = new StringWriter ();
    IOUtils.copy (url.openStream (), sw);
    return sw.getBuffer ().toString ();
}
",Copy File,Type-3 (WT3/4),TRUE
5263166,"protected AbstractUnicodeExtraField (String text, byte [] bytes, int off, int len) {
    CRC32 crc32 = new CRC32 ();
    crc32.update (bytes, off, len);
    nameCRC32 = crc32.getValue ();
    try {
        unicodeName = text.getBytes (""UTF-8"");
    } catch (UnsupportedEncodingException e) {
        throw new RuntimeException (""FATAL: UTF-8 encoding not supported."", e);
    }
}
",17506503,"static long computeFileCrc (File f) {
    FileInputStream fis = null;
    try {
        fis = new FileInputStream (f);
        CRC32 crc = new CRC32 ();
        byte [] data = new byte [BUFFER_SIZE];
        int len = - 1;
        while ((len = fis.read (data)) > - 1) {
            crc.update (data, 0, len);
        }
        return crc.getValue ();
    } catch (IOException e) {
        logger.error (""Unexpected exception while computing CRC on file: "" + f.getAbsolutePath (), e);
        return - 1;
    } finally {
        try {
            fis.close ();
        } catch (IOException e) {
        }
    }
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
2861198,"public static PO FactoryPO (Class < ? > c, Properties ctx, ResultSet rs, String trx) throws SecurityException, NoSuchMethodException, IllegalArgumentException, InstantiationException, IllegalAccessException, InvocationTargetException {
    Constructor < ? > con = c.getConstructor (Properties.class, ResultSet.class, String.class);
    PO p = (PO) con.newInstance (ctx, rs, trx);
    return p;
}
",2917117,"protected Object instantiate (Class < ? > type, Object [] args) {
    try {
        if (args.length == 0 || this.constructors.length == 0) return type.newInstance ();

        if (this.constructors.length == 1) if (this.constructors [0].getParameterTypes ().length == 0) return this.constructors [0].newInstance (new Object [0]);
        else return this.constructors [0].newInstance (args);

        else {
            Class < ? > [] types = new Class < ? > [args.length];
            for (int i = 0;
            i < args.length; i ++) types [i] = args [i].getClass ();

            try {
                return type.getConstructor (types).newInstance (args);
            } catch (NoSuchMethodException e) {
                return type.newInstance ();
            }
        }
    } catch (InstantiationException e) {
        throw new RuntimeException (instantiationError (type, ""It is probably a non-static inner class or an abstract class.""), e);
    } catch (IllegalAccessException e) {
        throw new RuntimeException (instantiationError (type, ""Either the class itself or its constructor are not public.""), e);
    } catch (IllegalArgumentException e) {
        List < String > types = new ArrayList < String > ();
        for (Object arg : args) types.add (arg.getClass ().getName ());

        throw new RuntimeException (instantiationError (type, ""Argument mismatch in calling the constructor with arguments."" + ""\nExpected types are (probably): "" + Arrays.asList (this.constructors [0].getParameterTypes ()) + ""\nProvided types are (sure): "" + types.toString ()), e);
    } catch (InvocationTargetException e) {
        throw new RuntimeException (instantiationError (type, ""Its construtor has thrown an exception, probably of type: "" + e.getCause () + "". See the stack trace for details""), e);
    }
}
",Instantiate Using Reflection,Type-3 (WT3/4),TRUE
10840966,"public void copy (String sourcePath, String targetPath) throws IOException {
    File sourceFile = new File (sourcePath);
    File targetFile = new File (targetPath);
    FileInputStream fileInputStream = null;
    FileOutputStream fileOutputStream = null;
    try {
        fileInputStream = new FileInputStream (sourceFile);
        fileOutputStream = new FileOutputStream (targetFile);
        byte [] buffer = new byte [4096];
        int bytesRead;
        while ((bytesRead = fileInputStream.read (buffer)) != - 1) fileOutputStream.write (buffer, 0, bytesRead);

    } finally {
        if (fileInputStream != null) try {
            fileInputStream.close ();
        } catch (IOException exception) {
            JOptionPane.showMessageDialog (null, AcideLanguageManager.getInstance ().getLabels ().getString (""s265"") + sourcePath, AcideLanguageManager.getInstance ().getLabels ().getString (""s266""), JOptionPane.ERROR_MESSAGE);
            AcideLog.getLog ().error (exception.getMessage ());
        }

        if (fileOutputStream != null) try {
            fileOutputStream.close ();
        } catch (IOException exception) {
            JOptionPane.showMessageDialog (null, AcideLanguageManager.getInstance ().getLabels ().getString (""s267"") + targetPath, AcideLanguageManager.getInstance ().getLabels ().getString (""268""), JOptionPane.ERROR_MESSAGE);
            AcideLog.getLog ().error (exception.getMessage ());
        }

    }
}
",23252484,"public static void copy (File file1, File file2) throws IOException {
    FileReader in = new FileReader (file1);
    FileWriter out = new FileWriter (file2);
    int c;
    while ((c = in.read ()) != - 1) out.write (c);

    in.close ();
    out.close ();
}
",Copy File,Type-3 (WT3/4),TRUE
1407918,"public CustomArticle NewInstance (NpsContext ctxt, Topic top, ResultSet rs) throws Exception {
    if (top == null) throw new NpsException (ErrorHelper.SYS_NOTOPIC);

    if (top.GetTable () == null || top.GetTable ().length () == 0) throw new NpsException (ErrorHelper.SYS_NEED_CUSTOM_TOPIC);

    String table_name = top.GetTable ().toUpperCase ();
    if (classes == null || classes.isEmpty () || ! classes.containsKey (table_name)) {
        return new CustomArticle (ctxt, top, rs);
    }
    Class clazz = GetArticleClass (table_name);
    java.lang.reflect.Constructor aconstructor = clazz.getConstructor (new Class [] {NpsContext.class, Topic.class, ResultSet.class});
    return (CustomArticle) aconstructor.newInstance (new Object [] {ctxt, top, rs});
}
",2218179,"private AppNode getAppNode (AppContext app) {
    AppDescriptor appDescriptor = app.getDescriptor ();
    ClassLoader classLoader = Thread.currentThread ().getContextClassLoader ();
    ImageIcon icon = null;
    try {
        String pkg = Tools.getPackage (appDescriptor.getClassName ());
        URL url = classLoader.getResource (pkg + ""/icon.png"");
        if (url == null) url = classLoader.getResource (""icon.png"");

        icon = new ImageIcon (new ImageIcon (url).getImage ().getScaledInstance (16, 16, Image.SCALE_SMOOTH));
    } catch (Exception ex) {
        Tools.logException (OptionsPanelManager.class, ex, ""Could not load icon "" + "" for app "" + appDescriptor.getClassName ());
    }
    if (! appDescriptor.isHME ()) {
        AppConfigurationPanel appConfigurationPanel = null;
        try {
            Class configurationPanel = classLoader.loadClass (appDescriptor.getConfigurationPanel ());
            Class [] parameters = new Class [1];
            parameters [0] = AppConfiguration.class;
            Constructor constructor = configurationPanel.getConstructor (parameters);
            AppConfiguration [] values = new AppConfiguration [1];
            values [0] = (AppConfiguration) app.getConfiguration ();
            appConfigurationPanel = (AppConfigurationPanel) constructor.newInstance ((Object []) values);
        } catch (Exception ex) {
            ex.printStackTrace ();
            Tools.logException (OptionsPanelManager.class, ex, ""Could not load configuration panel "" + appDescriptor.getConfigurationPanel () + "" for app "" + appDescriptor.getClassName ());
        }
        AppNode appNode = new AppNode (app, icon, appConfigurationPanel);
        return appNode;
    } else {
        return new AppNode (app, icon, new HMEConfigurationPanel (app.getConfiguration ()));
    }
}
",Instantiate Using Reflection,Type-3 (WT3/4),TRUE
12523607,"public void render (ServiceContext serviceContext) throws Exception {
    if (serviceContext.getTemplateName () == null) throw new Exception (""no Template defined for service: "" + serviceContext.getServiceInfo ().getRefName ());

    File f = new File (serviceContext.getTemplateName ());
    serviceContext.getResponse ().setContentLength ((int) f.length ());
    InputStream in = new FileInputStream (f);
    IOUtils.copy (in, serviceContext.getResponse ().getOutputStream (), 0, (int) f.length ());
    in.close ();
}
",13362846,"public static void setContenu (ContenuFichierElectronique contenuFichier, FichierElectronique fichierElectronique, UtilisateurIFGD utilisateurCourant) throws IOException, DocumentVideException {
    if (contenuFichier != null) {
        SupportDocument support = fichierElectronique.getSupport ();
        support.setFichierElectronique (fichierElectronique);
        FicheDocument ficheDocument = support.getFicheDocument ();
        String nomFichier = contenuFichier.getNomFichier ();
        String extension = FilenameUtils.getExtension (nomFichier);
        if (ficheDocument.getFichierElectronique (nomFichier) != null) {
            FichierElectronique fichierElectroniqueExistant = ficheDocument.getFichierElectronique (nomFichier);
            if (fichierElectroniqueExistant.getId () != null && ! fichierElectroniqueExistant.getId ().equals (fichierElectronique.getId ())) {
                throw new FichierElectroniqueExistantException (nomFichier, ficheDocument);
            }
        }
        if (fichierElectronique.getId () == null) {
            if (OfficeDocumentPropertiesUtil.canWriteIdIGID (extension)) {
                Long idIgid = OfficeDocumentPropertiesUtil.getIdIGID (contenuFichier);
                if (idIgid != null) {
                    throw new FichierElectroniqueExistantException (nomFichier, idIgid, ficheDocument);
                }
            }
        }
        InputStream inputStream = contenuFichier.getInputStream ();
        OutputStream outputStream = fichierElectronique.getOutputStream ();
        try {
            IOUtils.copy (inputStream, outputStream);
        } finally {
            try {
                inputStream.close ();
            } finally {
                outputStream.close ();
            }
        }
        String typeMime = contenuFichier.getContentType ();
        long tailleFichier = contenuFichier.getTailleFichier ();
        Date dateDerniereModification = new Date ();
        fichierElectronique.setNom (nomFichier);
        fichierElectronique.setTypeMime (extension);
        creerFormatSiNecessaire (typeMime, extension);
        fichierElectronique.setTaille (tailleFichier);
        fichierElectronique.setDateDerniereModification (dateDerniereModification);
        fichierElectronique.setSoumetteur (utilisateurCourant);
        if (extension.endsWith (""msg"")) {
            CourrielUtils.peuplerMetadonneesCourriel (fichierElectronique.getNom (), ficheDocument, contenuFichier.getInputStream (), utilisateurCourant);
        } else if (extension.endsWith (""eml"")) {
            Map < String, Object > properties = new GestionnaireProprietesMimeMessageParser ().parseMsg (contenuFichier.getInputStream ());
            CourrielUtils.peuplerMetadonneesCourriel (fichierElectronique.getNom (), ficheDocument, properties, utilisateurCourant);
        } else {
            FGDProprietesDocumentUtils.copierMetadonneesProprietes (fichierElectronique, ficheDocument);
        }

    }
}
",Copy File,Type-3 (WT3/4),TRUE
1977837,"public void copyFile (File sourceFile, String toDir, boolean create, boolean overwrite) throws FileNotFoundException, IOException {
    FileInputStream source = null;
    FileOutputStream destination = null;
    byte [] buffer;
    int bytes_read;
    File toFile = new File (toDir);
    if (create && ! toFile.exists ()) toFile.mkdirs ();

    if (toFile.exists ()) {
        File destFile = new File (toDir + ""/"" + sourceFile.getName ());
        try {
            if (! destFile.exists () || overwrite) {
                source = new FileInputStream (sourceFile);
                destination = new FileOutputStream (destFile);
                buffer = new byte [1024];
                while (true) {
                    bytes_read = source.read (buffer);
                    if (bytes_read == - 1) break;

                    destination.write (buffer, 0, bytes_read);
                }
            }
        } catch (Exception exx) {
            exx.printStackTrace ();
        } finally {
            if (source != null) try {
                source.close ();
            } catch (IOException e) {
            }

            if (destination != null) try {
                destination.close ();
            } catch (IOException e) {
            }

        }
    }
}
",11875445,"private static void loadFromZip () {
    InputStream in = Resources.class.getResourceAsStream (""data.zip"");
    if (in == null) {
        return;
    }
    ZipInputStream zipIn = new ZipInputStream (in);
    try {
        while (true) {
            ZipEntry entry = zipIn.getNextEntry ();
            if (entry == null) {
                break;
            }
            String entryName = entry.getName ();
            if (! entryName.startsWith (""/"")) {
                entryName = ""/"" + entryName;
            }
            ByteArrayOutputStream out = new ByteArrayOutputStream ();
            IOUtils.copy (zipIn, out);
            zipIn.closeEntry ();
            FILES.put (entryName, out.toByteArray ());
        }
        zipIn.close ();
    } catch (IOException e) {
        e.printStackTrace ();
    }
}
",Copy File,Type-3 (WT3/4),TRUE
482330,"public void convert (File src, File dest) throws IOException {
    InputStream in = new BufferedInputStream (new FileInputStream (src));
    DcmParser p = pfact.newDcmParser (in);
    Dataset ds = fact.newDataset ();
    p.setDcmHandler (ds.getDcmHandler ());
    try {
        FileFormat format = p.detectFileFormat ();
        if (format != FileFormat.ACRNEMA_STREAM) {
            System.out.println (""\n"" + src + "": not an ACRNEMA stream!"");
            return;
        }
        p.parseDcmFile (format, Tags.PixelData);
        if (ds.contains (Tags.StudyInstanceUID) || ds.contains (Tags.SeriesInstanceUID) || ds.contains (Tags.SOPInstanceUID) || ds.contains (Tags.SOPClassUID)) {
            System.out.println (""\n"" + src + "": contains UIDs!"" + "" => probable already DICOM - do not convert"");
            return;
        }
        boolean hasPixelData = p.getReadTag () == Tags.PixelData;
        boolean inflate = hasPixelData && ds.getInt (Tags.BitsAllocated, 0) == 12;
        int pxlen = p.getReadLength ();
        if (hasPixelData) {
            if (inflate) {
                ds.putUS (Tags.BitsAllocated, 16);
                pxlen = pxlen * 4 / 3;
            }
            if (pxlen != (ds.getInt (Tags.BitsAllocated, 0)>>> 3) * ds.getInt (Tags.Rows, 0) * ds.getInt (Tags.Columns, 0) * ds.getInt (Tags.NumberOfFrames, 1) * ds.getInt (Tags.NumberOfSamples, 1)) {
                System.out.println (""\n"" + src + "": mismatch pixel data length!"" + "" => do not convert"");
                return;
            }
        }
        ds.putUI (Tags.StudyInstanceUID, uid (studyUID));
        ds.putUI (Tags.SeriesInstanceUID, uid (seriesUID));
        ds.putUI (Tags.SOPInstanceUID, uid (instUID));
        ds.putUI (Tags.SOPClassUID, classUID);
        if (! ds.contains (Tags.NumberOfSamples)) {
            ds.putUS (Tags.NumberOfSamples, 1);
        }
        if (! ds.contains (Tags.PhotometricInterpretation)) {
            ds.putCS (Tags.PhotometricInterpretation, ""MONOCHROME2"");
        }
        if (fmi) {
            ds.setFileMetaInfo (fact.newFileMetaInfo (ds, UIDs.ImplicitVRLittleEndian));
        }
        OutputStream out = new BufferedOutputStream (new FileOutputStream (dest));
        try {
        } finally {
            ds.writeFile (out, encodeParam ());
            if (hasPixelData) {
                if (! skipGroupLen) {
                    out.write (PXDATA_GROUPLEN);
                    int grlen = pxlen + 8;
                    out.write ((byte) grlen);
                    out.write ((byte) (grlen>> 8));
                    out.write ((byte) (grlen>> 16));
                    out.write ((byte) (grlen>> 24));
                }
                out.write (PXDATA_TAG);
                out.write ((byte) pxlen);
                out.write ((byte) (pxlen>> 8));
                out.write ((byte) (pxlen>> 16));
                out.write ((byte) (pxlen>> 24));
            }
            if (inflate) {
                int b2, b3;
                for (; pxlen > 0; pxlen -= 3) {
                    out.write (in.read ());
                    b2 = in.read ();
                    b3 = in.read ();
                    out.write (b2 & 0x0f);
                    out.write (b2>> 4 | ((b3 & 0x0f) << 4));
                    out.write (b3>> 4);
                }
            } else {
                for (; pxlen > 0; -- pxlen) {
                    out.write (in.read ());
                }
            }
            out.close ();
        }
        System.out.print ('.');
    } finally {
        in.close ();
    }
}
",9257486,"public static boolean dumpFile (String from, File to, String lineBreak) {
    try {
        BufferedReader in = new BufferedReader (new InputStreamReader (new FileInputStream (from)));
        BufferedWriter out = new BufferedWriter (new OutputStreamWriter (new FileOutputStream (to)));
        String line = null;
        while ((line = in.readLine ()) != null) out.write (Main.getInstance ().resolve (line) + lineBreak);

        in.close ();
        out.close ();
    } catch (Exception e) {
        Installer.getInstance ().getLogger ().log (StringUtils.getStackTrace (e));
        return false;
    }
    return true;
}
",Copy File,Type-3 (WT3/4),TRUE
3265819,"@Test
public void testLargePut () throws Throwable {
    int size = CommonParameters.BLOCK_SIZE;
    InputStream is = new FileInputStream (_fileName);
    RepositoryFileOutputStream ostream = new RepositoryFileOutputStream (_nodeName, _putHandle, CommonParameters.local);
    int readLen = 0;
    int writeLen = 0;
    byte [] buffer = new byte [CommonParameters.BLOCK_SIZE];
    while ((readLen = is.read (buffer, 0, size)) != - 1) {
        ostream.write (buffer, 0, readLen);
        writeLen += readLen;
    }
    ostream.close ();
    CCNStats stats = _putHandle.getNetworkManager ().getStats ();
    Assert.assertEquals (0, stats.getCounter (""DeliverInterestFailed""));
}
",22900247,"public static void copyDirectory (File sourceDirectory, File targetDirectory) throws IOException {
    File [] sourceFiles = sourceDirectory.listFiles (FILE_FILTER);
    File [] sourceDirectories = sourceDirectory.listFiles (DIRECTORY_FILTER);
    targetDirectory.mkdirs ();
    if (sourceFiles != null && sourceFiles.length > 0) {
        for (int i = 0;
        i < sourceFiles.length; i ++) {
            File sourceFile = sourceFiles [i];
            FileInputStream fis = new FileInputStream (sourceFile);
            FileOutputStream fos = new FileOutputStream (targetDirectory + File.separator + sourceFile.getName ());
            FileChannel fcin = fis.getChannel ();
            FileChannel fcout = fos.getChannel ();
            ByteBuffer buf = ByteBuffer.allocateDirect (8192);
            long size = fcin.size ();
            long n = 0;
            while (n < size) {
                buf.clear ();
                if (fcin.read (buf) < 0) {
                    break;
                }
                buf.flip ();
                n += fcout.write (buf);
            }
            fcin.close ();
            fcout.close ();
            fis.close ();
            fos.close ();
        }
    }
    if (sourceDirectories != null && sourceDirectories.length > 0) {
        for (int i = 0;
        i < sourceDirectories.length; i ++) {
            File directory = sourceDirectories [i];
            File newTargetDirectory = new File (targetDirectory, directory.getName ());
            copyDirectory (directory, newTargetDirectory);
        }
    }
}
",Copy File,Type-3 (WT3/4),TRUE
10927176,"private static void recursivelyZipFiles (final String extension, String currentRelativePath, File currentDir, ZipOutputStream zipOutputStream) throws IOException {
    String [] files = currentDir.list (new FilenameFilter () {
        public boolean accept (File dir, String name) {
            File f = new File (dir, name);
            if (extension == null) return true;
            else return f.isDirectory () || name.endsWith (extension);

        }}

    );
    for (String filename : files) {
        File f = new File (currentDir, filename);
        String fileRelativePath = currentRelativePath + (Helper.isNullOrEmpty (currentRelativePath) ? """" : File.separator) + filename;
        if (f.isDirectory ()) recursivelyZipFiles (extension, fileRelativePath, f, zipOutputStream);
        else {
            BufferedInputStream in = null;
            byte [] data = new byte [1024];
            in = new BufferedInputStream (new FileInputStream (f), 1000);
            zipOutputStream.putNextEntry (new ZipEntry (fileRelativePath));
            int count;
            while ((count = in.read (data, 0, data.length)) != - 1) {
                zipOutputStream.write (data, 0, count);
            }
            zipOutputStream.closeEntry ();
        }
    }
}
",18348106,"public static File zipFile (File f, boolean absolutePaths, boolean deleteOriginal, boolean forceDelete, int level) throws IOException {
    if (! f.exists ()) {
        throw new FileNotFoundException (""file "" + f + "" does not exist"");
    }
    File destination = new File (f.getAbsolutePath () + "".zip"");
    if (destination.exists ()) {
        throw new IOException (""zipped file "" + destination + "" exists"");
    }
    ZipOutputStream zout = new ZipOutputStream (new BufferedOutputStream (new FileOutputStream (destination)));
    zout.setLevel (level);
    NSArray < File > files = f.isDirectory () ? arrayByAddingFilesInDirectory (f, true) : new NSArray < File > (f);
    try {
        BufferedInputStream origin = null;
        byte data [] = new byte [2048];
        for (int i = 0;
        i < files.count (); i ++) {
            File currentFile = files.objectAtIndex (i);
            FileInputStream fi = new FileInputStream (currentFile);
            origin = new BufferedInputStream (fi, 2048);
            String entryName = currentFile.getAbsolutePath ();
            if (! absolutePaths) {
                if (f.isDirectory ()) {
                    entryName = entryName.substring (f.getAbsolutePath ().length () + 1, entryName.length ());
                } else {
                    entryName = entryName.substring (f.getParentFile ().getAbsolutePath ().length () + 1, entryName.length ());
                }
            }
            ZipEntry entry = new ZipEntry (entryName);
            zout.putNextEntry (entry);
            int count;
            while ((count = origin.read (data, 0, 2048)) != - 1) {
                zout.write (data, 0, count);
            }
            origin.close ();
        }
        zout.close ();
    } catch (Exception e) {
        e.printStackTrace ();
    }
    if (deleteOriginal) {
        if (f.canWrite () || forceDelete) {
            if (! deleteDirectory (f)) {
                deleteDirectory (f);
            }
        }
    }
    return destination;
}
",Zip Files,Type-3 (WT3/4),TRUE
1184290,"@Override
public void execute () {
    File currentModelDirectory = new File (this.globalData.getData (String.class, GlobalData.MODEL_INSTALL_DIRECTORY));
    File mobileDirectory = new File (currentModelDirectory, ""mobile"");
    mobileDirectory.mkdir ();
    File mobileModelFile = new File (mobileDirectory, ""mobile_model.zip"");
    FileOutputStream outputStream = null;
    ZipOutputStream zipStream = null;
    BusinessModel businessModel = BusinessUnit.getInstance ().getBusinessModel ();
    try {
        mobileModelFile.createNewFile ();
        outputStream = new FileOutputStream (mobileModelFile);
        zipStream = new ZipOutputStream (outputStream);
        Dictionary dictionary = businessModel.getDictionary ();
        for (Definition definition : dictionary.getAllDefinitions ()) {
            ZipEntry entry = new ZipEntry (definition.getRelativeFileName ());
            zipStream.putNextEntry (entry);
            writeBinary (definition.getAbsoluteFileName (), zipStream);
        }
        final String modelFilename = ""model.xml"";
        ZipEntry entry = new ZipEntry (modelFilename);
        zipStream.putNextEntry (entry);
        writeBinary (businessModel.getAbsoluteFilename (modelFilename), zipStream);
        final String logoFilename = dictionary.getModel ().getImageSource (LogoType.mobile);
        entry = new ZipEntry (logoFilename);
        zipStream.putNextEntry (entry);
        writeBinary (businessModel.getAbsoluteFilename (logoFilename), zipStream);
    } catch (IOException e) {
        agentLogger.error (e);
    } finally {
        StreamHelper.close (zipStream);
        StreamHelper.close (outputStream);
    }
}
",4013457,"public int addDirectory (ZipOutputStream zosFile, File dirSource, String preSource) throws Exception {
    String ldirSource = dirSource.getName ();
    String lpreSource = preSource;
    int lcntEntries = 0;
    if (! (isRelativeDirectory ())) {
        ldirSource = dirSource.getAbsolutePath ();
        lpreSource = """";
    } else {
        ldirSource = dirSource.getName ();
        lpreSource = preSource;
    }
    File [] files = dirSource.listFiles ();
    for (int i = 0;
    i < files.length; i ++) {
        if (files [i].isDirectory () && isTraverseDirectory ()) {
            if (isRelativeDirectory ()) {
                lpreSource = lpreSource + File.separator + ldirSource;
                getLog ().debug (""Adding directory "" + lpreSource + File.separator + files [i].getName ());
                addDirectory (zosFile, files [i], lpreSource);
                lpreSource = preSource;
            } else {
                getLog ().debug (""Adding directory "" + ldirSource);
                addDirectory (zosFile, files [i], """");
            }
        } else if (! (files [i].isDirectory ())) {
            try {
                byte [] buffer = new byte [1024];
                FileInputStream fin = new FileInputStream (files [i]);
                if (isRelativeDirectory ()) {
                    getLog ().debug (""Adding file ["" + lpreSource + File.separator + ldirSource + File.separator + files [i].getName () + ""]"");
                    zosFile.putNextEntry (new ZipEntry (lpreSource + File.separator + ldirSource + File.separator + files [i].getName ()));
                } else {
                    getLog ().debug (""Adding file ["" + ldirSource + File.separator + files [i].getName () + ""]"");
                    zosFile.putNextEntry (new ZipEntry (ldirSource + File.separator + files [i].getName ()));
                }
                int length;
                while ((length = fin.read (buffer)) > 0) {
                    zosFile.write (buffer, 0, length);
                }
                zosFile.closeEntry ();
                fin.close ();
            } catch (IOException ioe) {
                getLog ().fatal (ioe);
                throw ioe;
            } catch (Exception ltheXcp) {
                getLog ().fatal (ltheXcp);
                throw ltheXcp;
            }
        }

        lcntEntries ++;
    }
    return lcntEntries;
}
",Zip Files,Type-3 (WT3/4),FALSE
3609806,"private static String getData (String myurl) throws Exception {
    System.out.println (""getdata"");
    URL url = new URL (myurl);
    uc = (HttpURLConnection) url.openConnection ();
    br = new BufferedReader (new InputStreamReader (uc.getInputStream ()));
    String temp = """", k = """";
    while ((temp = br.readLine ()) != null) {
        System.out.println (temp);
        k += temp;
    }
    br.close ();
    return k;
}
",14090536,"private String [] read (String path) throws Exception {
    final String [] names = {""index.txt"", """", ""index.html"", ""index.htm""};
    String [] list = null;
    for (int i = 0;
    i < names.length; i ++) {
        URL url = new URL (path + names [i]);
        try {
            BufferedReader in = new BufferedReader (new InputStreamReader (url.openStream ()));
            StringBuffer sb = new StringBuffer ();
            String s = null;
            while ((s = in.readLine ()) != null) {
                s = s.trim ();
                if (s.length () > 0) {
                    sb.append (s + ""\n"");
                }
            }
            in.close ();
            if (sb.indexOf (""<"") != - 1 && sb.indexOf ("">"") != - 1) {
                List links = LinkExtractor.scan (url, sb.toString ());
                HashSet set = new HashSet ();
                int prefixLen = path.length ();
                for (Iterator it = links.iterator ();
                it.hasNext ();) {
                    String link = it.next ().toString ();
                    if (! link.startsWith (path)) {
                        continue;
                    }
                    link = link.substring (prefixLen);
                    int idx = link.indexOf (""/"");
                    int idxq = link.indexOf (""?"");
                    if (idx > 0 && (idxq == - 1 || idx < idxq)) {
                        set.add (link.substring (0, idx + 1));
                    } else {
                        set.add (link);
                    }
                }
                list = (String []) set.toArray (new String [0]);
            } else {
                list = sb.toString ().split (""\n"");
            }
            return list;
        } catch (FileNotFoundException e) {
            e.printStackTrace ();
            continue;
        }
    }
    return new String [0];
}
",Download From Web,Type-3 (WT3/4),TRUE
2177123,"public void hyperlinkUpdate (HyperlinkEvent event) {
    URL url = event.getURL ();
    if (event.getEventType () == HyperlinkEvent.EventType.ENTERED && ! event.getDescription ().startsWith (""copyUrl:"")) {
        updatesEditorPane.setToolTipText (url.toString ());
    } else if (event.getEventType () == HyperlinkEvent.EventType.EXITED) {
        updatesEditorPane.setToolTipText (null);
    } else if (event.getEventType () == HyperlinkEvent.EventType.ACTIVATED) {
        if (event.getDescription ().startsWith (""copyUrl:"")) {
            String toCopy = event.getDescription ().replaceFirst (""copyUrl:"", """");
            StringSelection data = new StringSelection (toCopy);
            Clipboard clipboard = Toolkit.getDefaultToolkit ().getSystemClipboard ();
            clipboard.setContents (data, data);
        } else {
            String browser = configManager.getBrowser ();
            if (! Desktop.isDesktopSupported ()) {
                try {
                    if (! browser.equals ("""")) {
                        Runtime.getRuntime ().exec (browser + "" "" + url.toString ());
                    } else {
                        Runtime.getRuntime ().exec (""firefox "" + url.toString ());
                    }
                } catch (Exception ex) {
                    JOptionPane.showMessageDialog (this, ""Unable to find a web browser, please set up one on settings window"", ""Web browser error"", JOptionPane.WARNING_MESSAGE);
                }
            }
            try {
                Desktop desktop = Desktop.getDesktop ();
                URI uri = new URI (url.toString ());
                desktop.browse (uri);
            } catch (Exception e) {
                return;
            }
        }
    }

}
",6663397,"public void hyperlinkUpdate (HyperlinkEvent e) {
    if (e.getEventType () == HyperlinkEvent.EventType.ACTIVATED) {
        try {
            if (Desktop.isDesktopSupported ()) {
                Desktop.getDesktop ().browse (e.getURL ().toURI ());
            } else Tools.openURL (e.getURL ().toString ());

        } catch (Exception x) {
            JOptionPane.showMessageDialog (null, x.getMessage ());
        }
    }
}
",Open URL in System Browser,Type-3 (WT3/4),TRUE
5318545,"public static long calculateCheckSum (CharSequence data) {
    final Checksum checksummer = new CRC32 ();
    for (int i = 0;
    i < data.length (); i ++) {
        checksummer.update (data.charAt (i));
    }
    return checksummer.getValue ();
}
",16244025,"private byte [] gettEXtBytes (String keyword, String content) {
    byte [] keywordBytes = getISO8859_1Bytes (keyword);
    byte [] contentBytes = getISO8859_1Bytes (content);
    byte [] array = new byte [keywordBytes.length + contentBytes.length + 13];
    ByteBuffer buffer = ByteBuffer.wrap (array);
    buffer.putInt (keywordBytes.length + contentBytes.length + 1);
    buffer.put (getISO8859_1Bytes (CHUNK_TYPE_tEXT));
    buffer.put (keywordBytes);
    buffer.put ((byte) 0);
    buffer.put (contentBytes);
    CRC32 crc = new CRC32 ();
    crc.update (array, 4, keywordBytes.length + contentBytes.length + 5);
    buffer.putInt ((int) crc.getValue ());
    return array;
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
44949,"private static void readAndRewrite (File inFile, File outFile) throws IOException {
    ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile)));
    DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis);
    Dataset ds = DcmObjectFactory.getInstance ().newDataset ();
    dcmParser.setDcmHandler (ds.getDcmHandler ());
    dcmParser.parseDcmFile (null, Tags.PixelData);
    PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    System.out.println (""reading "" + inFile + ""..."");
    pdReader.readPixelData (false);
    ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile)));
    DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE;
    ds.writeDataset (out, dcmEncParam);
    ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ());
    System.out.println (""writing "" + outFile + ""..."");
    PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    pdWriter.writePixelData ();
    out.flush ();
    out.close ();
    System.out.println (""done!"");
}
",81287,"public void convert (File src, File dest) throws IOException {
    InputStream in = new BufferedInputStream (new FileInputStream (src));
    DcmParser p = pfact.newDcmParser (in);
    Dataset ds = fact.newDataset ();
    p.setDcmHandler (ds.getDcmHandler ());
    try {
        FileFormat format = p.detectFileFormat ();
        if (format != FileFormat.ACRNEMA_STREAM) {
            System.out.println (""\n"" + src + "": not an ACRNEMA stream!"");
            return;
        }
        p.parseDcmFile (format, Tags.PixelData);
        if (ds.contains (Tags.StudyInstanceUID) || ds.contains (Tags.SeriesInstanceUID) || ds.contains (Tags.SOPInstanceUID) || ds.contains (Tags.SOPClassUID)) {
            System.out.println (""\n"" + src + "": contains UIDs!"" + "" => probable already DICOM - do not convert"");
            return;
        }
        boolean hasPixelData = p.getReadTag () == Tags.PixelData;
        boolean inflate = hasPixelData && ds.getInt (Tags.BitsAllocated, 0) == 12;
        int pxlen = p.getReadLength ();
        if (hasPixelData) {
            if (inflate) {
                ds.putUS (Tags.BitsAllocated, 16);
                pxlen = pxlen * 4 / 3;
            }
            if (pxlen != (ds.getInt (Tags.BitsAllocated, 0)>>> 3) * ds.getInt (Tags.Rows, 0) * ds.getInt (Tags.Columns, 0) * ds.getInt (Tags.NumberOfFrames, 1) * ds.getInt (Tags.NumberOfSamples, 1)) {
                System.out.println (""\n"" + src + "": mismatch pixel data length!"" + "" => do not convert"");
                return;
            }
        }
        ds.putUI (Tags.StudyInstanceUID, uid (studyUID));
        ds.putUI (Tags.SeriesInstanceUID, uid (seriesUID));
        ds.putUI (Tags.SOPInstanceUID, uid (instUID));
        ds.putUI (Tags.SOPClassUID, classUID);
        if (! ds.contains (Tags.NumberOfSamples)) {
            ds.putUS (Tags.NumberOfSamples, 1);
        }
        if (! ds.contains (Tags.PhotometricInterpretation)) {
            ds.putCS (Tags.PhotometricInterpretation, ""MONOCHROME2"");
        }
        if (fmi) {
            ds.setFileMetaInfo (fact.newFileMetaInfo (ds, UIDs.ImplicitVRLittleEndian));
        }
        OutputStream out = new BufferedOutputStream (new FileOutputStream (dest));
        try {
        } finally {
            ds.writeFile (out, encodeParam ());
            if (hasPixelData) {
                if (! skipGroupLen) {
                    out.write (PXDATA_GROUPLEN);
                    int grlen = pxlen + 8;
                    out.write ((byte) grlen);
                    out.write ((byte) (grlen>> 8));
                    out.write ((byte) (grlen>> 16));
                    out.write ((byte) (grlen>> 24));
                }
                out.write (PXDATA_TAG);
                out.write ((byte) pxlen);
                out.write ((byte) (pxlen>> 8));
                out.write ((byte) (pxlen>> 16));
                out.write ((byte) (pxlen>> 24));
            }
            if (inflate) {
                int b2, b3;
                for (; pxlen > 0; pxlen -= 3) {
                    out.write (in.read ());
                    b2 = in.read ();
                    b3 = in.read ();
                    out.write (b2 & 0x0f);
                    out.write (b2>> 4 | ((b3 & 0x0f) << 4));
                    out.write (b3>> 4);
                }
            } else {
                for (; pxlen > 0; -- pxlen) {
                    out.write (in.read ());
                }
            }
            out.close ();
        }
        System.out.print ('.');
    } finally {
        in.close ();
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1287483,"protected void doGet (HttpServletRequest req, HttpServletResponse response) throws ServletException, IOException {
    keysString = req.getParameter (""resultKeys"");
    if (req.getParameter (""mode"") != null && ! req.getParameter (""mode"").equals ("""")) {
        archiveHelper.setMode (req.getParameter (""mode""));
    }
    SecurityAdvisor secAdvisor = null;
    try {
        secAdvisor = (SecurityAdvisor) req.getSession ().getAttribute (SecurityAdvisor.SECURITY_ADVISOR_SESSION_KEY);
        if (secAdvisor != null) {
            response.setContentType (""application/x-download"");
            response.setHeader (""Content-Disposition"", ""attachment;filename=microarray.zip"");
            response.setHeader (""Cache-Control"", ""max-age=0, must-revalidate"");
            long time1 = System.currentTimeMillis ();
            Session sess = secAdvisor.getHibernateSession (req.getUserPrincipal () != null ? req.getUserPrincipal ().getName () : ""guest"");
            DictionaryHelper dh = DictionaryHelper.getInstance (sess);
            baseDir = dh.getAnalysisReadDirectory (req.getServerName ());
            archiveHelper.setTempDir (dh.getPropertyDictionary (PropertyDictionary.TEMP_DIRECTORY));
            Map fileNameMap = new HashMap ();
            long compressedFileSizeTotal = getFileNamesToDownload (baseDir, keysString, fileNameMap);
            ZipOutputStream zipOut = null;
            TarArchiveOutputStream tarOut = null;
            if (archiveHelper.isZipMode ()) {
                zipOut = new ZipOutputStream (response.getOutputStream ());
            } else {
                tarOut = new TarArchiveOutputStream (response.getOutputStream ());
            }
            int totalArchiveSize = 0;
            for (Iterator i = fileNameMap.keySet ().iterator ();
            i.hasNext ();) {
                String analysisNumber = (String) i.next ();
                Analysis analysis = null;
                List analysisList = sess.createQuery (""SELECT a from Analysis a where a.number = '"" + analysisNumber + ""'"").list ();
                if (analysisList.size () == 1) {
                    analysis = (Analysis) analysisList.get (0);
                }
                if (analysis == null) {
                    log.error (""Unable to find request "" + analysisNumber + "".  Bypassing download for user "" + req.getUserPrincipal ().getName () + ""."");
                    continue;
                }
                if (! secAdvisor.canRead (analysis)) {
                    log.error (""Insufficient permissions to read analysis "" + analysisNumber + "".  Bypassing download for user "" + req.getUserPrincipal ().getName () + ""."");
                    continue;
                }
                List fileNames = (List) fileNameMap.get (analysisNumber);
                for (Iterator i1 = fileNames.iterator ();
                i1.hasNext ();) {
                    String filename = (String) i1.next ();
                    String zipEntryName = ""bioinformatics-analysis-"" + filename.substring (baseDir.length ());
                    archiveHelper.setArchiveEntryName (zipEntryName);
                    TransferLog xferLog = new TransferLog ();
                    xferLog.setFileName (filename.substring (baseDir.length () + 5));
                    xferLog.setStartDateTime (new java.util.Date (System.currentTimeMillis ()));
                    xferLog.setTransferType (TransferLog.TYPE_DOWNLOAD);
                    xferLog.setTransferMethod (TransferLog.METHOD_HTTP);
                    xferLog.setPerformCompression (""Y"");
                    xferLog.setIdAnalysis (analysis.getIdAnalysis ());
                    xferLog.setIdLab (analysis.getIdLab ());
                    InputStream in = archiveHelper.getInputStreamToArchive (filename, zipEntryName);
                    ZipEntry zipEntry = null;
                    if (archiveHelper.isZipMode ()) {
                        zipEntry = new ZipEntry (archiveHelper.getArchiveEntryName ());
                        zipOut.putNextEntry (zipEntry);
                    } else {
                        TarArchiveEntry entry = new TarArchiveEntry (archiveHelper.getArchiveEntryName ());
                        entry.setSize (archiveHelper.getArchiveFileSize ());
                        tarOut.putArchiveEntry (entry);
                    }
                    OutputStream out = null;
                    if (archiveHelper.isZipMode ()) {
                        out = zipOut;
                    } else {
                        out = tarOut;
                    }
                    int size = archiveHelper.transferBytes (in, out);
                    totalArchiveSize += size;
                    xferLog.setFileSize (new BigDecimal (size));
                    xferLog.setEndDateTime (new java.util.Date (System.currentTimeMillis ()));
                    sess.save (xferLog);
                    if (archiveHelper.isZipMode ()) {
                        zipOut.closeEntry ();
                        totalArchiveSize += zipEntry.getCompressedSize ();
                    } else {
                        tarOut.closeArchiveEntry ();
                        totalArchiveSize += archiveHelper.getArchiveFileSize ();
                    }
                    archiveHelper.removeTemporaryFile ();
                }
                sess.flush ();
            }
            response.setContentLength (totalArchiveSize);
            if (archiveHelper.isZipMode ()) {
                zipOut.finish ();
                zipOut.flush ();
            } else {
                tarOut.close ();
                tarOut.flush ();
            }
        } else {
            response.setStatus (999);
            System.out.println (""DownloadAnalyisFolderServlet: You must have a SecurityAdvisor in order to run this command."");
        }
    } catch (Exception e) {
        response.setStatus (999);
        System.out.println (""DownloadAnalyisFolderServlet: An exception occurred "" + e.toString ());
        e.printStackTrace ();
    } finally {
        if (secAdvisor != null) {
            try {
                secAdvisor.closeHibernateSession ();
            } catch (Exception e) {
            }
        }
        archiveHelper.removeTemporaryFile ();
    }
}
",9318114,"private void writeClassFile (File zipFile, ZipOutputStream out, JAssembler asm) {
    ClassDef def = asm.def;
    Box box = asm.classFile;
    String path = def.ns.replace ('.', '/') + '/' + def.name + "".class"";
    try {
        out.putNextEntry (new ZipEntry (path));
        out.write (box.buf, 0, box.len);
        out.closeEntry ();
    } catch (IOException e) {
        throw err (""Cannot write zip entry "" + path, zipFile);
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
2721038,"public File copyFile (File f) throws IOException {
    File t = createNewFile (""fm"", ""cpy"");
    FileOutputStream fos = new FileOutputStream (t);
    FileChannel foc = fos.getChannel ();
    FileInputStream fis = new FileInputStream (f);
    FileChannel fic = fis.getChannel ();
    foc.transferFrom (fic, 0, fic.size ());
    foc.close ();
    fic.close ();
    return t;
}
",10287986,"public static boolean encodeFileToFile (String infile, String outfile) {
    boolean success = false;
    java.io.InputStream in = null;
    java.io.OutputStream out = null;
    try {
        in = new Base64.InputStream (new java.io.BufferedInputStream (new java.io.FileInputStream (infile)), Base64.ENCODE);
        out = new java.io.BufferedOutputStream (new java.io.FileOutputStream (outfile));
        byte [] buffer = new byte [65536];
        int read = - 1;
        while ((read = in.read (buffer)) >= 0) {
            out.write (buffer, 0, read);
        }
        success = true;
    } catch (java.io.IOException exc) {
        exc.printStackTrace ();
    } finally {
        try {
            in.close ();
        } catch (Exception exc) {
        }
        try {
            out.close ();
        } catch (Exception exc) {
        }
    }
    return success;
}
",Copy File,Type-3 (WT3/4),TRUE
160739,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",20601765,"private static void addToZip (File [] files, ZipOutputStream out) throws IOException {
    byte [] buf = new byte [1024];
    for (int i = 0;
    i < files.length; i ++) {
        if (files [i].isDirectory ()) {
            addToZip (files [i].listFiles (), out);
        } else {
            FileInputStream in = new FileInputStream (files [i]);
            out.putNextEntry (new ZipEntry (files [i].getPath ()));
            int len;
            while ((len = in.read (buf)) > 0) {
                out.write (buf, 0, len);
            }
            out.closeEntry ();
            in.close ();
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
6430125,"protected Object openDialogBox (Control cellEditorWindow) {
    FileDialog dialog = new FileDialog (parent.getShell (), SWT.OPEN);
    dialog.setFilterExtensions (new String [] {""*.jpg;*.JPG;*.JPEG;*.gif;*.GIF;*.png;*.PNG"", ""*.jpg;*.JPG;*.JPEG"", ""*.gif;*.GIF"", ""*.png;*.PNG""});
    dialog.setFilterNames (new String [] {""All"", ""Joint Photographic Experts Group (JPEG)"", ""Graphics Interchange Format (GIF)"", ""Portable Network Graphics (PNG)""});
    String imagePath = dialog.open ();
    if (imagePath == null) return null;

    IProject project = ProjectManager.getInstance ().getCurrentProject ();
    String projectFolderPath = project.getLocation ().toOSString ();
    File imageFile = new File (imagePath);
    String fileName = imageFile.getName ();
    ImageData imageData = null;
    try {
        imageData = new ImageData (imagePath);
    } catch (SWTException e) {
        UserErrorException error = new UserErrorException (PropertyHandler.getInstance ().getProperty (""_invalid_image_title""), PropertyHandler.getInstance ().getProperty (""_invalid_image_text""));
        UserErrorService.INSTANCE.showError (error);
        return null;
    }
    if (imageData == null) {
        UserErrorException error = new UserErrorException (PropertyHandler.getInstance ().getProperty (""_invalid_image_title""), PropertyHandler.getInstance ().getProperty (""_invalid_image_text""));
        UserErrorService.INSTANCE.showError (error);
        return null;
    }
    File copiedImageFile = new File (projectFolderPath + File.separator + imageFolderPath + File.separator + fileName);
    if (copiedImageFile.exists ()) {
        Path path = new Path (copiedImageFile.getPath ());
        copiedImageFile = new File (projectFolderPath + File.separator + imageFolderPath + File.separator + UUID.randomUUID ().toString () + ""."" + path.getFileExtension ());
    }
    try {
        copiedImageFile.createNewFile ();
    } catch (IOException e1) {
        ExceptionHandlingService.INSTANCE.handleException (e1);
        copiedImageFile = null;
    }
    if (copiedImageFile == null) {
        copiedImageFile = new File (projectFolderPath + File.separator + imageFolderPath + File.separator + UUID.randomUUID ().toString ());
        try {
            copiedImageFile.createNewFile ();
        } catch (IOException e) {
            ExceptionHandlingService.INSTANCE.handleException (e);
            return """";
        }
    }
    FileReader in = null;
    FileWriter out = null;
    try {
        in = new FileReader (imageFile);
        out = new FileWriter (copiedImageFile);
        int c;
        while ((c = in.read ()) != - 1) out.write (c);

        in.close ();
        out.close ();
    } catch (FileNotFoundException e) {
        ExceptionHandlingService.INSTANCE.handleException (e);
        return """";
    } catch (IOException e) {
        ExceptionHandlingService.INSTANCE.handleException (e);
        return """";
    }
    return imageFolderPath + File.separator + copiedImageFile.getName ();
}
",10824317,"public static void copyFile (File from, File to) throws Exception {
    if (! from.exists ()) return;

    FileInputStream in = new FileInputStream (from);
    FileOutputStream out = new FileOutputStream (to);
    byte [] buffer = new byte [8192];
    int bytes_read;
    while (true) {
        bytes_read = in.read (buffer);
        if (bytes_read == - 1) break;

        out.write (buffer, 0, bytes_read);
    }
    out.flush ();
    out.close ();
    in.close ();
}
",Copy File,Type-3 (WT3/4),TRUE
15595627,"private float [] [] Transpose (float [] [] a) {
    if (INFO) {
        System.out.println (""Performing Transpose..."");
    }
    float m [] [] = new float [a [0].length] [a.length];
    for (int i = 0;
    i < a.length; i ++) for (int j = 0;
    j < a [i].length; j ++) m [j] [i] = a [i] [j];

    return m;
}
",21505623,"private void updateWeightAnalog (int trackID, int k, float ts, boolean increase) {
    if (increase) {
        float targetV = neurons [trackID].getV (ts);
        float otherV = neurons [k].getV (ts);
        float targetMean = neurons [trackID].getMeanActivation ();
        float otherMean = neurons [k].getMeanActivation ();
        float delta1 = otherV * (otherV - otherMean) * targetV;
        float delta2 = targetV * (targetV - targetMean) * otherV;
        float mDelta = sigmoid ((delta1 + delta2) / 2.0f);
        w [trackID] [k] += alpha * mDelta;
        if (w [trackID] [k] > 1.0f) w [trackID] [k] = 1.0f;

        w [k] [trackID] = w [trackID] [k];
    } else {
        w [trackID] [k] -= reduceW;
        if (w [trackID] [k] < - 1.0f) w [trackID] [k] = - 1.0f;

        w [k] [trackID] = w [trackID] [k];
    }
}
",Transpose a Matrix.,Type-3 (WT3/4),TRUE
5102752,"public String stringOfUrl (String addr) throws IOException {
    ByteArrayOutputStream output = new ByteArrayOutputStream ();
    URL url = new URL (addr);
    IOUtils.copy (url.openStream (), output);
    return output.toString ();
}
",11092394,"private void copy (final File file) throws IOException {
    String targetFilename = targetFilename (file);
    FileInputStream fis = new FileInputStream (file);
    try {
        FileChannel source = fis.getChannel ();
        try {
            FileOutputStream fos = new FileOutputStream (targetFilename);
            try {
                FileChannel target = fos.getChannel ();
                try {
                    target.transferFrom (source, 0, source.size ());
                } finally {
                    target.close ();
                }
            } finally {
                fos.close ();
            }
        } finally {
            source.close ();
        }
    } finally {
        fis.close ();
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1903107,"private void writeEntry (JarOutputStream jos, ZipEntry entry, InputStream data) throws IOException {
    jos.putNextEntry (entry);
    byte [] newBytes = InputStreamUtil.createReadBuffer ();
    int size = data.read (newBytes);
    while (size != - 1) {
        jos.write (newBytes, 0, size);
        size = data.read (newBytes);
    }
    data.close ();
}
",8305219,"@Override
protected void handleFile (File file, int depth, Collection results) throws IOException {
    String path = """";
    File parent = file.getParentFile ();
    for (int i = 0;
    i < depth - 1; i ++) {
        path = parent.getName () + ""/"" + path;
        parent = parent.getParentFile ();
    }
    ZipEntry entry = new ZipEntry (path + file.getName ());
    output.putNextEntry (entry);
    int size = (int) file.length ();
    byte [] buffer = new byte [size];
    FileInputStream fis = new FileInputStream (file);
    fis.read (buffer);
    output.write (buffer);
}
",Zip Files,Type-3 (WT3/4),TRUE
1282532,"void initOut () throws IOException {
    if (zipped) {
        zout = new ZipOutputStream (sink);
        zout.putNextEntry (new ZipEntry (""file.xml""));
        this.xout = new OutputStreamWriter (zout, ""UTF8"");
    } else {
        this.xout = new OutputStreamWriter (sink, ""UTF8"");
    }
}
",10062086,"private void addToJar (JarOutputStream out, InputStream in, String entryName, long length) throws IOException {
    byte [] buf = new byte [2048];
    ZipEntry entry = new ZipEntry (entryName);
    CRC32 crc = new CRC32 ();
    entry.setSize (length);
    entry.setCrc (crc.getValue ());
    out.putNextEntry (entry);
    int read = in.read (buf);
    while (read > 0) {
        crc.update (buf, 0, read);
        out.write (buf, 0, read);
        read = in.read (buf);
    }
    entry.setCrc (crc.getValue ());
    in.close ();
    out.closeEntry ();
}
",Zip Files,Type-3 (WT3/4),FALSE
1093295,"private static void createZip (final File destinationFile, final List < File > files, final int cutFileNameIndex) throws IOException {
    final ZipOutputStream oStream = new ZipOutputStream (new FileOutputStream (destinationFile));
    for (final File file : files) {
        final String fullFileName = file.getAbsolutePath ();
        final String cuttedFileName = fullFileName.substring (cutFileNameIndex);
        final String osIndependendFileName = cuttedFileName.replace (File.separatorChar, '/');
        oStream.putNextEntry (new ZipEntry (osIndependendFileName));
        final FileInputStream iStream = new FileInputStream (file);
        FileOperations.copy (iStream, oStream);
        oStream.closeEntry ();
        iStream.close ();
    }
    oStream.close ();
}
",9609404,"private void addFile (ZipOutputStream zos, String path, Element details, String name) throws Exception {
    ZipEntry entry = new ZipEntry (name);
    zos.putNextEntry (entry);
    BinaryFile.write (details, zos);
    zos.closeEntry ();
}
",Zip Files,Type-3 (WT3/4),FALSE
61823,"public void mousePressed (MouseEvent e) {
    if (e.getClickCount () == 2) {
        String S, S2, S3, Temp;
        int i;
        String [] projstr;
        switch (ListCommande.getSelectedIndex ()) {
            case 0 :
            case 12 :
                S = JOptionPane.showInputDialog (null, ""Entrez le message"", ""Message"", 1);
                if (S != null) {
                    S = ""'"" + S;
                    if (ListCommande.getSelectedIndex () == 0) {
                        Temp = """";
                        if (JOptionPane.showConfirmDialog (null, ""Voulez vous positionner le message?"", ""Option"", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE) == JOptionPane.YES_OPTION) {
                            jump = new JumpTo (null, true);
                            Temp = jump.Ed_X.getText () + "","" + jump.Ed_Y.getText ();
                            jump.dispose ();
                            jump = new JumpTo (null, false);
                            jump.setVisible (false);
                            jump.setModal (true);
                            jump.setTitle (""Largeur/Hauteur"");
                            jump.LblX.setText (""W"");
                            jump.LblY.setText (""H"");
                            jump.setVisible (true);
                            Temp += "","" + jump.Ed_X.getText () + "","" + jump.Ed_Y.getText () + "","";
                            jump.dispose ();
                            S = Temp + S;
                        }
                        Ed_Commande.setText (""Message("" + S + ""')"");
                    }
                    if (ListCommande.getSelectedIndex () == 12) Ed_Commande.setText (""OnResultQuery('"" + S + ""')"");

                }
                break;
            case 1 :
                cd = new CondDecl (projet, """", null, true);
                if (cd.status == 1) Ed_Commande.setText (""Condition('"" + cd.Commande + ""')"");

                cd.dispose ();
                break;
            case 2 :
            case 3 :
                values = new String [projet.getObjets ().size ()];
                for (int j = 0;
                j < projet.getObjets ().size (); j ++) values [j] = projet.getObjetByIndex (j).Name;

                liste = new JListe (values, null, ""Choisissez l'objet"", true);
                if (liste.status == 1) {
                    S = ""1"";
                    S = (String) JOptionPane.showInputDialog (null, ""Entrez la quantité de l'objet"", ""Quantité"", 1, null, null, S);
                    if (S != null) {
                        if (S.compareTo ("""") != 0) {
                            if (S.compareTo (""1"") == 0) {
                                if (ListCommande.getSelectedIndex () == 2) Ed_Commande.setText (""AddObject("" + liste.ListBox.getSelectedValue ().toString () + "")"");
                                else Ed_Commande.setText (""DelObject("" + liste.ListBox.getSelectedValue ().toString () + "")"");

                            } else {
                                if (ListCommande.getSelectedIndex () == 2) Ed_Commande.setText (""AddObject("" + liste.ListBox.getSelectedValue ().toString () + "","" + S + "")"");
                                else Ed_Commande.setText (""DelObject("" + liste.ListBox.getSelectedValue ().toString () + "","" + S + "")"");

                            }
                        }
                    }
                }
                liste.dispose ();
                break;
            case 4 :
            case 5 :
                ArrayList < Carte > carte = projet.getCartes ();
                ArrayList < String > nomcarte = new ArrayList < String > ();
                for (i = 0; i < carte.size (); i ++) nomcarte.add (carte.get (i).Name);

                projstr = new String [nomcarte.size ()];
                projstr = nomcarte.toArray (projstr);
                liste = new JListe (projstr, null, ""Choisissez la carte"", true);
                if (liste.status == 1) {
                    jump = new JumpTo (null, true);
                    if (jump.status == 1) {
                        if (ListCommande.getSelectedIndex () == 4) Ed_Commande.setText (""Teleport("" + liste.ListBox.getSelectedValue ().toString () + "","" + jump.Ed_X.getText () + "","" + jump.Ed_Y.getText () + "")"");
                        else Ed_Commande.setText (""ChangeResPoint("" + liste.ListBox.getSelectedValue ().toString () + "","" + jump.Ed_X.getText () + "","" + jump.Ed_Y.getText () + "")"");

                    }
                    jump.dispose ();
                }
                liste.dispose ();
                break;
            case 6 :
                jump = new JumpTo (null, true);
                if (jump.status == 1) Ed_Commande.setText (""SScroll("" + jump.Ed_X.getText () + "","" + jump.Ed_Y.getText () + "")"");

                jump.dispose ();
                break;
            case 7 :
                ArrayList < String > nomclasses = new ArrayList < String > ();
                for (i = 0; i < projet.getClassesJoueur ().size (); i ++) nomclasses.add (projet.getClassesJoueur ().get (i).Name);

                projstr = new String [nomclasses.size ()];
                projstr = nomclasses.toArray (projstr);
                liste = new JListe (projstr, null, ""Choisissez la classe(vide=aucune)"", true);
                if (liste.status == 1) {
                    Ed_Commande.setText (""ChangeClasse('"" + liste.ListBox.getSelectedValue ().toString () + ""')"");
                }
                break;
            case 8 :
            case 17 :
            case 19 :
            case 20 :
            case 21 :
                JFileChooser choix = new JFileChooser ();
                if (ListCommande.getSelectedIndex () == 7) choix.setCurrentDirectory (new java.io.File (projet.getName () + ""/Chipset/""));
                else choix.setCurrentDirectory (new java.io.File (projet.getName () + ""/Sound/""));

                int retour = choix.showOpenDialog (null);
                if (retour == JFileChooser.APPROVE_OPTION) {
                    switch (ListCommande.getSelectedIndex ()) {
                        case 8 :
                            Ed_Commande.setText (""ChangeSkin('Chipset\\"" + choix.getSelectedFile ().getName () + ""')"");
                            break;
                        case 17 :
                            Ed_Commande.setText (""PlayMusic('Sound\\"" + choix.getSelectedFile ().getName () + ""')"");
                            break;
                        case 29 :
                            Ed_Commande.setText (""PlaySound('Sound\\"" + choix.getSelectedFile ().getName () + ""')"");
                            break;
                        case 20 :
                            Ed_Commande.setText (""ChAttaqueSound('Sound\\"" + choix.getSelectedFile ().getName () + ""')"");
                            break;
                        case 21 :
                            Ed_Commande.setText (""ChBlesseSound('Sound\\"" + choix.getSelectedFile ().getName () + ""')"");
                            break;
                    }
                }
                break;
            case 9 :
                values = new String [projet.getMonstres ().size ()];
                for (int j = 0;
                j < projet.getMonstres ().size (); j ++) values [j] = projet.getMonstreByIndex (j).Name;

                liste = new JListe (values, null, ""Choisissez le monstre"", true);
                if (liste.status == 1) {
                    jump = new JumpTo (null, true);
                    if (jump.status == 1) {
                        S = JOptionPane.showInputDialog (null, ""Entrez le nombre de Monstre"", ""Monstre"", 1);
                        if (S != null) {
                            S2 = JOptionPane.showInputDialog (null, ""Vitesse de respawn?(0=ne respawn pas)"", ""Monstre"", 1);
                            if (S2 != null) {
                                S3 = JOptionPane.showInputDialog (null, ""Monstres donnent de l'xp? (0=non, 1=oui)"", ""Monstre"", 1);
                                if (S3 != null) {
                                    Ed_Commande.setText (""GenereMonstre("" + liste.ListBox.getSelectedValue ().toString () + "","" + jump.Ed_X.getText () + "","" + jump.Ed_Y.getText () + "","" + S + "","" + S2 + "","" + S3 + "")"");
                                }
                            }
                        }
                    }
                    jump.dispose ();
                }
                liste.dispose ();
                break;
            case 11 :
                Temp = """";
                if (JOptionPane.showConfirmDialog (null, ""Voulez vous positionner le query?"", ""Option"", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE) == JOptionPane.YES_OPTION) {
                    jump = new JumpTo (null, true);
                    if (jump.status == 1) Temp = ""InputQuery("" + jump.Ed_X.getText () + "","" + jump.Ed_Y.getText ();

                    jump.dispose ();
                }
                S = JOptionPane.showInputDialog (null, ""Entrez la question"", ""Message"", 1);
                if (S != null) {
                    i = 0;
                    if (Temp.compareTo ("""") == 0) Temp = ""InputQuery('"" + S + ""'"";
                    else Temp += "",'"" + S + ""'"";

                    do {
                        S = """";
                        S = JOptionPane.showInputDialog (null, ""Entrez la réponse "" + (i + 1), ""Message"", 1);
                        if (S == null) S = """";

                        if (S != """") Temp += "",'"" + S + ""'"";

                        i ++;
                    } while (S != """");
                    Temp += "")"";
                    Ed_Commande.setText (Temp);
                }
                break;
            case 14 :
                S = JOptionPane.showInputDialog (null, ""Entrez la question"", ""Message"", 1);
                if (S != null) Ed_Commande.setText (Ed_Commande.getText () + ""InputString('"" + S + ""')"");

                break;
            case 15 :
                S = JOptionPane.showInputDialog (null, ""Entrez le message du magasin"", ""Message"", 1);
                if (S != null) {
                    values = new String [projet.getObjets ().size ()];
                    for (int j = 0;
                    j < projet.getObjets ().size (); j ++) values [j] = projet.getObjetByIndex (j).Name;

                    liste = new JListe (values, null, ""Choisissez les objets"", true);
                    if (liste.status == 1) {
                        Ed_Commande.setText (""Magasin('"" + S + ""'"");
                        Object [] obj = liste.ListBox.getSelectedValues ();
                        for (int j = 0;
                        j < obj.length; j ++) Ed_Commande.setText (Ed_Commande.getText () + "",'"" + obj [j].toString () + ""'"");

                        Ed_Commande.setText (Ed_Commande.getText () + "")"");
                    }
                    liste.dispose ();
                }
                break;
            case 16 :
                S = JOptionPane.showInputDialog (null, ""Entrez le temps d'attente"", ""Timer"", 1);
                if (S != null) Ed_Commande.setText (""Attente("" + S + "")"");

                break;
            case 22 :
            case 23 :
                values = new String [projet.getMagies ().size ()];
                for (int j = 0;
                j < projet.getMagies ().size (); j ++) values [j] = projet.getMagieByIndex (j).Name;

                liste = new JListe (values, null, ""Choisissez la magie"", true);
                if (liste.status == 1) {
                    if (ListCommande.getSelectedIndex () == 23) Ed_Commande.setText (""AddMagie("" + liste.ListBox.getSelectedValue ().toString () + "")"");
                    else Ed_Commande.setText (""DelMagie("" + liste.ListBox.getSelectedValue ().toString () + "")"");

                }
                liste.dispose ();
                break;
            case 26 :
            case 27 :
                S = JOptionPane.showInputDialog (null, ""Entrez le nom de la sauvegarde(Vide = Choix du joueur)"", ""Sauvegarde"", 1);
                if (S != null) {
                    if (ListCommande.getSelectedIndex () == 27) Ed_Commande.setText (""Chargement('"" + S + ""')"");
                    else Ed_Commande.setText (""Sauvegarde('"" + S + ""')"");

                }
                break;
            case 33 :
            case 34 :
                projstr = new String [verifie.getMenuPossibles ().size ()];
                projstr = verifie.getMenuPossibles ().toArray (projstr);
                liste = new JListe (projstr, null, ""Choisissez le menu"", true);
                if (liste.status == 1) {
                    if (ListCommande.getSelectedIndex () == 32) Ed_Commande.setText (""AddMenu("" + liste.ListBox.getSelectedValue ().toString () + "")"");
                    else Ed_Commande.setText (""DelMenu("" + liste.ListBox.getSelectedValue ().toString () + "")"");

                }
                break;
            default :
                Ed_Commande.setText (Ed_Commande.getText () + ListCommande.getSelectedValue ().toString ());
        }
    }
}
",280540,"private void readNormalButtonActionPerformed (java.awt.event.ActionEvent evt) {
    int returnVal = fc.showOpenDialog (this);
    if (returnVal == JFileChooser.APPROVE_OPTION) {
        input = fc.getSelectedFile ();
    } else return;

    try {
        FileInputStream fis = new FileInputStream (input);
        InputStreamReader isr = new InputStreamReader (fis, ""UTF8"");
        BufferedReader uni = new BufferedReader (isr);
        String line = """", s = """";
        while (line != null) {
            line = uni.readLine ();
            if (line != null) {
                s += line + ""\n"";
            }
        }
        jTextArea1.setText (s);
        jTextPane1.setText (s);
    } catch (Exception ex) {
        String oops = ex.toString ();
    }
}
",File Dialog,Type-3 (WT3/4),TRUE
413237,"public void convert (File src, File dest) throws IOException {
    InputStream in = new BufferedInputStream (new FileInputStream (src));
    DcmParser p = pfact.newDcmParser (in);
    Dataset ds = fact.newDataset ();
    p.setDcmHandler (ds.getDcmHandler ());
    try {
        FileFormat format = p.detectFileFormat ();
        if (format != FileFormat.ACRNEMA_STREAM) {
            System.out.println (""\n"" + src + "": not an ACRNEMA stream!"");
            return;
        }
        p.parseDcmFile (format, Tags.PixelData);
        if (ds.contains (Tags.StudyInstanceUID) || ds.contains (Tags.SeriesInstanceUID) || ds.contains (Tags.SOPInstanceUID) || ds.contains (Tags.SOPClassUID)) {
            System.out.println (""\n"" + src + "": contains UIDs!"" + "" => probable already DICOM - do not convert"");
            return;
        }
        boolean hasPixelData = p.getReadTag () == Tags.PixelData;
        boolean inflate = hasPixelData && ds.getInt (Tags.BitsAllocated, 0) == 12;
        int pxlen = p.getReadLength ();
        if (hasPixelData) {
            if (inflate) {
                ds.putUS (Tags.BitsAllocated, 16);
                pxlen = pxlen * 4 / 3;
            }
            if (pxlen != (ds.getInt (Tags.BitsAllocated, 0)>>> 3) * ds.getInt (Tags.Rows, 0) * ds.getInt (Tags.Columns, 0) * ds.getInt (Tags.NumberOfFrames, 1) * ds.getInt (Tags.NumberOfSamples, 1)) {
                System.out.println (""\n"" + src + "": mismatch pixel data length!"" + "" => do not convert"");
                return;
            }
        }
        ds.putUI (Tags.StudyInstanceUID, uid (studyUID));
        ds.putUI (Tags.SeriesInstanceUID, uid (seriesUID));
        ds.putUI (Tags.SOPInstanceUID, uid (instUID));
        ds.putUI (Tags.SOPClassUID, classUID);
        if (! ds.contains (Tags.NumberOfSamples)) {
            ds.putUS (Tags.NumberOfSamples, 1);
        }
        if (! ds.contains (Tags.PhotometricInterpretation)) {
            ds.putCS (Tags.PhotometricInterpretation, ""MONOCHROME2"");
        }
        if (fmi) {
            ds.setFileMetaInfo (fact.newFileMetaInfo (ds, UIDs.ImplicitVRLittleEndian));
        }
        OutputStream out = new BufferedOutputStream (new FileOutputStream (dest));
        try {
        } finally {
            ds.writeFile (out, encodeParam ());
            if (hasPixelData) {
                if (! skipGroupLen) {
                    out.write (PXDATA_GROUPLEN);
                    int grlen = pxlen + 8;
                    out.write ((byte) grlen);
                    out.write ((byte) (grlen>> 8));
                    out.write ((byte) (grlen>> 16));
                    out.write ((byte) (grlen>> 24));
                }
                out.write (PXDATA_TAG);
                out.write ((byte) pxlen);
                out.write ((byte) (pxlen>> 8));
                out.write ((byte) (pxlen>> 16));
                out.write ((byte) (pxlen>> 24));
            }
            if (inflate) {
                int b2, b3;
                for (; pxlen > 0; pxlen -= 3) {
                    out.write (in.read ());
                    b2 = in.read ();
                    b3 = in.read ();
                    out.write (b2 & 0x0f);
                    out.write (b2>> 4 | ((b3 & 0x0f) << 4));
                    out.write (b3>> 4);
                }
            } else {
                for (; pxlen > 0; -- pxlen) {
                    out.write (in.read ());
                }
            }
            out.close ();
        }
        System.out.print ('.');
    } finally {
        in.close ();
    }
}
",3660402,"public void importCertFile (File file) throws IOException {
    File kd;
    File cd;
    synchronized (this) {
        kd = keysDir;
        cd = certsDir;
    }
    if (! cd.isDirectory ()) {
        kd.mkdirs ();
        cd.mkdirs ();
    }
    String newName = file.getName ();
    File dest = new File (cd, newName);
    FileChannel sourceChannel = null;
    FileChannel destinationChannel = null;
    try {
        sourceChannel = new FileInputStream (file).getChannel ();
        destinationChannel = new FileOutputStream (dest).getChannel ();
        sourceChannel.transferTo (0, sourceChannel.size (), destinationChannel);
    } finally {
        if (sourceChannel != null) {
            try {
                sourceChannel.close ();
            } catch (IOException e) {
            }
        }
        if (destinationChannel != null) {
            try {
                destinationChannel.close ();
            } catch (IOException e) {
            }
        }
    }
}
",Copy File,Type-3 (WT3/4),TRUE
468954,"private byte [] getFileContents (String fileName) throws Exception {
    ByteArrayOutputStream ba = new ByteArrayOutputStream ();
    FileInputStream fis = new FileInputStream (fileName);
    byte [] data = new byte [1024];
    int read = fis.read (data, 0, 1024);
    while (read > - 1) {
        ba.write (data, 0, read);
        read = fis.read (data, 0, 1024);
    }
    fis.close ();
    return ba.toByteArray ();
}
",6033123,"public static boolean unZip (String zipname, String extractTo) {
    InputStream is;
    ZipInputStream zis;
    try {
        is = new FileInputStream (extractTo + zipname);
        zis = new ZipInputStream (new BufferedInputStream (is));
        ZipEntry ze;
        while ((ze = zis.getNextEntry ()) != null) {
            ByteArrayOutputStream baos = new ByteArrayOutputStream ();
            byte [] buffer = new byte [1024];
            int count;
            String filename = ze.getName ();
            FileOutputStream fout = new FileOutputStream (extractTo + filename);
            while ((count = zis.read (buffer)) != - 1) {
                baos.write (buffer, 0, count);
                byte [] bytes = baos.toByteArray ();
                fout.write (bytes);
                baos.reset ();
            }
            fout.flush ();
            fout.close ();
            zis.closeEntry ();
        }
        zis.close ();
    } catch (IOException e) {
        e.printStackTrace ();
        return false;
    }
    return true;
}
",Load File into Byte Array,Type-3 (WT3/4),TRUE
469518,"public synchronized void writeFile (String filename) throws IOException {
    int amount;
    byte buffer [] = new byte [4096];
    File f = new File (filename);
    FileInputStream in = new FileInputStream (f);
    putNextEntry (new ZipEntry (f.getName ()));
    while ((amount = in.read (buffer)) != - 1) write (buffer, 0, amount);

    closeEntry ();
    in.close ();
}
",16171577,"private void zipTempDir (String dir2zip, ZipOutputStream zos) {
    try {
        File zipDir = new File (dir2zip);
        String [] dirList = zipDir.list ();
        byte [] readBuffer = new byte [2156];
        int bytesIn = 0;
        for (int i = 0;
        i < dirList.length; i ++) {
            File f = new File (zipDir, dirList [i]);
            if (f.isDirectory ()) {
                String filePath = f.getPath ();
                zipTempDir (filePath, zos);
                continue;
            }
            FileInputStream fis = new FileInputStream (f);
            String filePath = f.getPath ();
            filePath = getZipPath (filePath);
            ZipEntry anEntry = new ZipEntry (filePath);
            zos.putNextEntry (anEntry);
            while ((bytesIn = fis.read (readBuffer)) != - 1) {
                zos.write (readBuffer, 0, bytesIn);
            }
            fis.close ();
        }
    } catch (Exception e) {
        System.out.println (""Could not do the zipDir process. debug zipDir()"");
        System.out.println (""This would be an internal variable configuration error. I guess you'll have to debug it"");
        e.printStackTrace ();
        System.exit (1);
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
732800,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",9744794,"public static void saveToZipFile (File f, ByteBuffer buf) {
    try {
        FileOutputStream fOut = new FileOutputStream (f);
        ZipOutputStream zipOut = new ZipOutputStream (fOut);
        zipOut.putNextEntry (new ZipEntry (""contents""));
        zipOut.write (buf.getBytes ());
        zipOut.closeEntry ();
        zipOut.close ();
        fOut.close ();
    } catch (Exception e) {
        e.printStackTrace ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
778875,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",10287019,"public static File fileToZipFile (File file) throws Exception {
    ZipOutputStream out = null;
    FileInputStream in = null;
    File retFile = changeFileNameSuffix (file, ""zip"");
    try {
        byte [] buf = new byte [1024];
        out = new ZipOutputStream (new FileOutputStream (retFile));
        in = new FileInputStream (file);
        out.putNextEntry (new ZipEntry (file.getName ()));
        int len;
        while ((len = in.read (buf)) > 0) {
            out.write (buf, 0, len);
        }
        out.closeEntry ();
    } finally {
        if (in != null) {
            in.close ();
        }
        if (out != null) {
            out.close ();
        }
    }
    file.delete ();
    return retFile;
}
",Zip Files,Type-3 (WT3/4),FALSE
2238218,"public void includeCss (Group group, Writer out, PageContext pageContext) throws IOException {
    ByteArrayOutputStream outtmp = new ByteArrayOutputStream ();
    if (AbstractGroupBuilder.getInstance ().buildGroupJsIfNeeded (group, outtmp, pageContext.getServletContext ())) {
        FileOutputStream fileStream = null;
        try {
            fileStream = new FileOutputStream (new File (RetentionHelper.buildFullRetentionFilePath (group, "".css"")));
            IOUtils.copy (new ByteArrayInputStream (outtmp.toByteArray ()), fileStream);
        } finally {
            if (fileStream != null) fileStream.close ();

        }
    }
}
",9857695,"private void copyArtifact (String name) throws IOException {
    IOUtils.copyFromClassPath (name, model.getOutputFolder () + name);
}
",Copy File,Type-3 (WT3/4),TRUE
892279,"File zip (File dir, File zipFile) throws IOException {
    ZipOutputStream zipOut = new ZipOutputStream (new FileOutputStream (zipFile));
    for (File file : dir.listFiles ()) {
        if (file.isFile ()) {
            byte [] data = new byte [(int) file.length ()];
            DataInputStream in = new DataInputStream (new FileInputStream (file));
            in.readFully (data);
            in.close ();
            zipOut.putNextEntry (new ZipEntry (file.getName ()));
            zipOut.write (data, 0, data.length);
            zipOut.closeEntry ();
        }
    }
    zipOut.close ();
    return zipFile;
}
",18517649,"void signJar (String jarName, String alias, String [] args) throws Exception {
    boolean aliasUsed = false;
    X509Certificate tsaCert = null;
    if (sigfile == null) {
        sigfile = alias;
        aliasUsed = true;
    }
    if (sigfile.length () > 8) {
        sigfile = sigfile.substring (0, 8).toUpperCase (Locale.ENGLISH);
    } else {
        sigfile = sigfile.toUpperCase (Locale.ENGLISH);
    }
    StringBuilder tmpSigFile = new StringBuilder (sigfile.length ());
    for (int j = 0;
    j < sigfile.length (); j ++) {
        char c = sigfile.charAt (j);
        if (! ((c >= 'A' && c <= 'Z') || (c >= '0' && c <= '9') || (c == '-') || (c == '_'))) {
            if (aliasUsed) {
                c = '_';
            } else {
                throw new RuntimeException (rb.getString (""signature filename must consist of the following characters: A-Z, 0-9, _ or -""));
            }
        }
        tmpSigFile.append (c);
    }
    sigfile = tmpSigFile.toString ();
    String tmpJarName;
    if (signedjar == null) tmpJarName = jarName + "".sig"";
    else tmpJarName = signedjar;

    File jarFile = new File (jarName);
    File signedJarFile = new File (tmpJarName);
    try {
        zipFile = new ZipFile (jarName);
    } catch (IOException ioe) {
        error (rb.getString (""unable to open jar file: "") + jarName, ioe);
    }
    FileOutputStream fos = null;
    try {
        fos = new FileOutputStream (signedJarFile);
    } catch (IOException ioe) {
        error (rb.getString (""unable to create: "") + tmpJarName, ioe);
    }
    PrintStream ps = new PrintStream (fos);
    ZipOutputStream zos = new ZipOutputStream (ps);
    String sfFilename = (META_INF + sigfile + "".SF"").toUpperCase (Locale.ENGLISH);
    String bkFilename = (META_INF + sigfile + "".DSA"").toUpperCase (Locale.ENGLISH);
    Manifest manifest = new Manifest ();
    Map < String, Attributes > mfEntries = manifest.getEntries ();
    Attributes oldAttr = null;
    boolean mfModified = false;
    boolean mfCreated = false;
    byte [] mfRawBytes = null;
    try {
        MessageDigest digests [] = {MessageDigest.getInstance (digestalg)};
        ZipEntry mfFile;
        if ((mfFile = getManifestFile (zipFile)) != null) {
            mfRawBytes = getBytes (zipFile, mfFile);
            manifest.read (new ByteArrayInputStream (mfRawBytes));
            oldAttr = (Attributes) (manifest.getMainAttributes ().clone ());
        } else {
            Attributes mattr = manifest.getMainAttributes ();
            mattr.putValue (Attributes.Name.MANIFEST_VERSION.toString (), ""1.0"");
            String javaVendor = System.getProperty (""java.vendor"");
            String jdkVersion = System.getProperty (""java.version"");
            mattr.putValue (""Created-By"", jdkVersion + "" ("" + javaVendor + "")"");
            mfFile = new ZipEntry (JarFile.MANIFEST_NAME);
            mfCreated = true;
        }
        BASE64Encoder encoder = new JarBASE64Encoder ();
        Vector < ZipEntry > mfFiles = new Vector < ZipEntry > ();
        for (Enumeration < ? extends ZipEntry > enum_ = zipFile.entries ();
        enum_.hasMoreElements ();) {
            ZipEntry ze = enum_.nextElement ();
            if (ze.getName ().startsWith (META_INF)) {
                mfFiles.addElement (ze);
                if (signatureRelated (ze.getName ())) {
                    continue;
                }
            }
            if (manifest.getAttributes (ze.getName ()) != null) {
                if (updateDigests (ze, zipFile, digests, encoder, manifest) == true) {
                    mfModified = true;
                }
            } else if (! ze.isDirectory ()) {
                Attributes attrs = getDigestAttributes (ze, zipFile, digests, encoder);
                mfEntries.put (ze.getName (), attrs);
                mfModified = true;
            }

        }
        if (mfModified) {
            ByteArrayOutputStream baos = new ByteArrayOutputStream ();
            manifest.write (baos);
            byte [] newBytes = baos.toByteArray ();
            if (mfRawBytes != null && oldAttr.equals (manifest.getMainAttributes ())) {
                int newPos = findHeaderEnd (newBytes);
                int oldPos = findHeaderEnd (mfRawBytes);
                if (newPos == oldPos) {
                    System.arraycopy (mfRawBytes, 0, newBytes, 0, oldPos);
                } else {
                    byte [] lastBytes = new byte [oldPos + newBytes.length - newPos];
                    System.arraycopy (mfRawBytes, 0, lastBytes, 0, oldPos);
                    System.arraycopy (newBytes, newPos, lastBytes, oldPos, newBytes.length - newPos);
                    newBytes = lastBytes;
                }
            }
            mfRawBytes = newBytes;
        }
        if (mfModified) {
            mfFile = new ZipEntry (JarFile.MANIFEST_NAME);
        }
        if (verbose != null) {
            if (mfCreated) {
                System.out.println (rb.getString (""   adding: "") + mfFile.getName ());
            } else if (mfModified) {
                System.out.println (rb.getString ("" updating: "") + mfFile.getName ());
            }

        }
        zos.putNextEntry (mfFile);
        zos.write (mfRawBytes);
        ManifestDigester manDig = new ManifestDigester (mfRawBytes);
        SignatureFile sf = new SignatureFile (digests, manifest, manDig, sigfile, signManifest);
        if (tsaAlias != null) {
            tsaCert = getTsaCert (tsaAlias);
        }
        SignatureFile.Block block = null;
        try {
            block = sf.generateBlock (privateKey, sigalg, certChain, externalSF, tsaUrl, tsaCert, signingMechanism, args, zipFile);
        } catch (SocketTimeoutException e) {
            error (rb.getString (""unable to sign jar: "") + rb.getString (""no response from the Timestamping Authority. "") + rb.getString (""When connecting from behind a firewall then an HTTP proxy may need to be specified. "") + rb.getString (""Supply the following options to jarsigner: "") + ""\n  -J-Dhttp.proxyHost=<hostname> "" + ""\n  -J-Dhttp.proxyPort=<portnumber> "", e);
        }
        sfFilename = sf.getMetaName ();
        bkFilename = block.getMetaName ();
        ZipEntry sfFile = new ZipEntry (sfFilename);
        ZipEntry bkFile = new ZipEntry (bkFilename);
        long time = System.currentTimeMillis ();
        sfFile.setTime (time);
        bkFile.setTime (time);
        zos.putNextEntry (sfFile);
        sf.write (zos);
        if (verbose != null) {
            if (zipFile.getEntry (sfFilename) != null) {
                System.out.println (rb.getString ("" updating: "") + sfFilename);
            } else {
                System.out.println (rb.getString (""   adding: "") + sfFilename);
            }
        }
        if (verbose != null) {
            if (tsaUrl != null || tsaCert != null) {
                System.out.println (rb.getString (""requesting a signature timestamp""));
            }
            if (tsaUrl != null) {
                System.out.println (rb.getString (""TSA location: "") + tsaUrl);
            }
            if (tsaCert != null) {
                String certUrl = TimestampedSigner.getTimestampingUrl (tsaCert);
                if (certUrl != null) {
                    System.out.println (rb.getString (""TSA location: "") + certUrl);
                }
                System.out.println (rb.getString (""TSA certificate: "") + printCert ("""", tsaCert, false, 0));
            }
            if (signingMechanism != null) {
                System.out.println (rb.getString (""using an alternative signing mechanism""));
            }
        }
        zos.putNextEntry (bkFile);
        block.write (zos);
        if (verbose != null) {
            if (zipFile.getEntry (bkFilename) != null) {
                System.out.println (rb.getString ("" updating: "") + bkFilename);
            } else {
                System.out.println (rb.getString (""   adding: "") + bkFilename);
            }
        }
        for (int i = 0;
        i < mfFiles.size (); i ++) {
            ZipEntry ze = mfFiles.elementAt (i);
            if (! ze.getName ().equalsIgnoreCase (JarFile.MANIFEST_NAME) && ! ze.getName ().equalsIgnoreCase (sfFilename) && ! ze.getName ().equalsIgnoreCase (bkFilename)) {
                writeEntry (zipFile, zos, ze);
            }
        }
        for (Enumeration < ? extends ZipEntry > enum_ = zipFile.entries ();
        enum_.hasMoreElements ();) {
            ZipEntry ze = enum_.nextElement ();
            if (! ze.getName ().startsWith (META_INF)) {
                if (verbose != null) {
                    if (manifest.getAttributes (ze.getName ()) != null) System.out.println (rb.getString (""  signing: "") + ze.getName ());
                    else System.out.println (rb.getString (""   adding: "") + ze.getName ());

                }
                writeEntry (zipFile, zos, ze);
            }
        }
    } catch (IOException ioe) {
        error (rb.getString (""unable to sign jar: "") + ioe, ioe);
    } finally {
        if (zipFile != null) {
            zipFile.close ();
            zipFile = null;
        }
        if (zos != null) {
            zos.close ();
        }
    }
    if (signedjar == null) {
        if (! signedJarFile.renameTo (jarFile)) {
            File origJar = new File (jarName + "".orig"");
            if (jarFile.renameTo (origJar)) {
                if (signedJarFile.renameTo (jarFile)) {
                    origJar.delete ();
                } else {
                    MessageFormat form = new MessageFormat (rb.getString (""attempt to rename signedJarFile to jarFile failed""));
                    Object [] source = {signedJarFile, jarFile};
                    error (form.format (source));
                }
            } else {
                MessageFormat form = new MessageFormat (rb.getString (""attempt to rename jarFile to origJar failed""));
                Object [] source = {jarFile, origJar};
                error (form.format (source));
            }
        }
    }
    if (hasExpiredCert || hasExpiringCert || notYetValidCert || badKeyUsage || badExtendedKeyUsage || badNetscapeCertType || chainNotValidated) {
        System.out.println ();
        System.out.println (rb.getString (""Warning: ""));
        if (badKeyUsage) {
            System.out.println (rb.getString (""The signer certificate's KeyUsage extension doesn't allow code signing.""));
        }
        if (badExtendedKeyUsage) {
            System.out.println (rb.getString (""The signer certificate's ExtendedKeyUsage extension doesn't allow code signing.""));
        }
        if (badNetscapeCertType) {
            System.out.println (rb.getString (""The signer certificate's NetscapeCertType extension doesn't allow code signing.""));
        }
        if (hasExpiredCert) {
            System.out.println (rb.getString (""The signer certificate has expired.""));
        } else if (hasExpiringCert) {
            System.out.println (rb.getString (""The signer certificate will expire within six months.""));
        } else if (notYetValidCert) {
            System.out.println (rb.getString (""The signer certificate is not yet valid.""));
        }

        if (chainNotValidated) {
            System.out.println (rb.getString (""The signer's certificate chain is not validated.""));
        }
    }
}
",Zip Files,Type-3 (WT3/4),TRUE
16930290,"public void writeTo (OutputStream out) throws IOException {
    IOUtils.copy (tempFile.getInputStream (), out);
}
",21715891,"protected void copy (File src, File dest) throws IOException {
    if (src.isDirectory () && dest.isFile ()) throw new IOException (""Cannot copy a directory to a file"");

    if (src.isDirectory ()) {
        File newDir = new File (dest, src.getName ());
        if (! newDir.mkdirs ()) throw new IOException (""Cannot create a new Directory"");

        File [] entries = src.listFiles ();
        for (int i = 0;
        i < entries.length; ++ i) copy (entries [i], newDir);

        return;
    }
    if (dest.isDirectory ()) {
        File newFile = new File (dest, src.getName ());
        newFile.createNewFile ();
        copy (src, newFile);
        return;
    }
    try {
        if (src.length () == 0) {
            dest.createNewFile ();
            return;
        }
        FileChannel fc = new FileInputStream (src).getChannel ();
        FileChannel dstChannel = new FileOutputStream (dest).getChannel ();
        long transfered = 0;
        long totalLength = src.length ();
        while (transfered < totalLength) {
            long num = fc.transferTo (transfered, totalLength - transfered, dstChannel);
            if (num == 0) throw new IOException (""Error while copying"");

            transfered += num;
        }
        dstChannel.close ();
        fc.close ();
    } catch (IOException e) {
        if (os.equals (""Unix"")) {
            _logger.fine (""Trying to use cp to copy file..."");
            File cp = new File (""/usr/bin/cp"");
            if (! cp.exists ()) cp = new File (""/bin/cp"");

            if (! cp.exists ()) cp = new File (""/usr/local/bin/cp"");

            if (! cp.exists ()) cp = new File (""/sbin/cp"");

            if (! cp.exists ()) cp = new File (""/usr/sbin/cp"");

            if (! cp.exists ()) cp = new File (""/usr/local/sbin/cp"");

            if (cp.exists ()) {
                Process cpProcess = Runtime.getRuntime ().exec (cp.getAbsolutePath () + "" '"" + src.getAbsolutePath () + ""' '"" + dest.getAbsolutePath () + ""'"");
                int errCode;
                try {
                    errCode = cpProcess.waitFor ();
                } catch (java.lang.InterruptedException ie) {
                    throw e;
                }
                return;
            }
        }
        throw e;
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1409148,"public static int save () {
    try {
        String filename = ""tyrant.sav"";
        FileDialog fd = new FileDialog (new Frame (), ""Save Game"", FileDialog.SAVE);
        fd.setFile (filename);
        fd.setVisible (true);
        if (fd.getFile () != null) {
            filename = fd.getDirectory () + fd.getFile ();
        } else {
            return 0;
        }
        FileOutputStream f = new FileOutputStream (filename);
        ZipOutputStream z = new ZipOutputStream (f);
        z.putNextEntry (new ZipEntry (""data.xml""));
        if (! save (new ObjectOutputStream (z))) {
            throw new Error (""Save game failed"");
        }
        Game.message (""Game saved - "" + filename);
        z.closeEntry ();
        z.close ();
        if (saveHasBeenCalledAlready) Game.message (""Please note that you can only restore the game with the same version of Tyrant (v"" + VERSION + "")."");

        saveHasBeenCalledAlready = false;
    } catch (Exception e) {
        Game.message (""Error while saving: "" + e.toString ());
        if (QuestApp.isapplet) {
            Game.message (""This may be due to your browser security restrictions"");
            Game.message (""If so, run the web start or downloaded application version instead"");
        }
        System.out.println (e);
        return - 1;
    }
    return 1;
}
",19534212,"@SuppressWarnings(""unchecked"")
public void doGetZip (HashMap < String, String > args, HttpServletResponse res) throws ServletException, IOException {
    try {
        int dayIdFrom = Integer.parseInt (args.get (""dateFrom""));
        int dayIdTo = Integer.parseInt (args.get (""dateTo""));
        WDCDay dateFrom = new WDCDay (dayIdFrom);
        WDCDay dateTo = new WDCDay (dayIdTo);
        DateInterval dateInterval = new DateInterval (dateFrom, dateTo);
        String dataTimeFormat = args.get (""timeFormat"");
        int sampling = 0;
        String s = args.get (""sampling"");
        if (s != null) {
            sampling = Integer.parseInt (s);
        }
        String parameters = args.get (""param"");
        String [] paramArray = parameters.split ("";"");
        long curTime = (new java.util.Date ()).getTime ();
        res.addHeader (""content-disposition"", ""attachment; filename=spidr_"" + curTime + "".zip"");
        Connection con = null;
        Statement stmt = null;
        WDCTable metaElem = null;
        try {
            con = ConnectionPool.getConnection (""metadata"");
            stmt = con.createStatement ();
            metaElem = new WDCTable (stmt, SQL_LOAD_META_ELEMENTS);
            stmt.close ();
        } finally {
            try {
                ConnectionPool.releaseConnection (con);
            } catch (Exception ignore) {
            }
        }
        LocalApi api = new LocalApi ();
        DataSequenceSet dss = new DataSequenceSet ("""");
        for (int i = 0;
        i < paramArray.length; i ++) {
            Vector < ? > p = getParameter (paramArray [i]);
            String elem = (String) p.get (0);
            String table = (String) p.get (1);
            String station = (String) p.get (2);
            Station stn = null;
            if (station != null) {
                stn = new Station (station, table, """");
            }
            int indElemElement = metaElem.getColumnIndex (""element"");
            int indElemTable = metaElem.getColumnIndex (""elemTable"");
            int indElemDescription = metaElem.getColumnIndex (""description"");
            int indElemMultiplier = metaElem.getColumnIndex (""multiplier"");
            int indElemMissingValue = metaElem.getColumnIndex (""missingValue"");
            int indElemUnits = metaElem.getColumnIndex (""units"");
            int elInd = metaElem.findRow (indElemTable, table, indElemElement, elem);
            String elemDescr = (String) metaElem.getValueAt (elInd, indElemDescription);
            String elemUnits = (String) metaElem.getValueAt (elInd, indElemUnits);
            float multiplier = Float.parseFloat ((String) metaElem.getValueAt (elInd, indElemMultiplier));
            float missingValue = Float.parseFloat ((String) metaElem.getValueAt (elInd, indElemMissingValue));
            DataDescription descr = new DataDescription (table, elem, """", elemDescr, elemUnits, elem);
            descr.setMultiplier (multiplier);
            descr.setMissingValue (missingValue);
            Vector < ? > v = api.getData (descr, stn, dateInterval, sampling);
            if (v != null && v.size () != 0) {
                DataSequence ds = (DataSequence) v.get (0);
                dss.add (ds);
            }
        }
        for (int i = 0;
        i < dss.size (); i ++) {
            String group = """";
            DailyData dd = null;
            try {
                dd = (DailyData) ((DataSequence) dss.elementAt (i)).elementAt (0);
                DataDescription ddescr = dd.getDescription ();
                String table = ddescr.getTable ();
                String [] groupList = Utilities.splitString (Settings.get (""viewGroups.groupOrder""));
                boolean flag = false;
                for (int k = 0;
                (k < groupList.length) && ! flag; k ++) {
                    String [] tables = UpdateMetadata.getTablesForGroup (groupList [k]);
                    for (int j = 0;
                    (j < tables.length) && ! flag; j ++) {
                        if (tables [j].equals (table)) {
                            flag = true;
                            group = groupList [k];
                        }
                    }
                }
            } catch (Exception e) {
                log.error (""Unexpected error: "" + e.toString ());
            }
            ZipOutputStream zos = new ZipOutputStream (res.getOutputStream ());
            for (int j = 0;
            j <= dss.size (); j ++) {
                dd = (DailyData) ((DataSequence) dss.elementAt (i)).elementAt (0);
                try {
                    String spidrServerName = Settings.get (""sites.localSite"");
                    String spidrServerUrl = Settings.get (""sites."" + spidrServerName + "".url"");
                    String metadataCollection = Settings.get (""viewGroups."" + group + "".metadataCollection"");
                    String fileUrl = spidrServerUrl + (spidrServerUrl.endsWith (""/"") ? """" : ""/"") + ""osproxy.do?specialRequest=document&docId="" + metadataCollection + dd.getStation ().getStn ().split (""_"") [0];
                    BufferedReader in = new BufferedReader (new InputStreamReader ((new URL (fileUrl)).openStream ()));
                    zos.putNextEntry (new ZipEntry (dd.getStation ().getStn () + "".xml""));
                    int buf;
                    while ((buf = in.read ()) != - 1) {
                        zos.write (buf);
                    }
                    in.close ();
                } catch (Exception e) {
                    log.error (""Couldn't add metadata to ZIP file: "" + e.toString ());
                }
            }
            String entryFileName = ""spidr_"" + curTime + ""_"" + i + "".txt"";
            zos.putNextEntry (new ZipEntry (entryFileName));
            PrintWriter plt = new PrintWriter (zos);
            if (log.isDebugEnabled ()) {
                log.debug (""asciiExportDataSet() files are ready"");
            }
            String dateFormat = ""yyyy-MM-dd HH:mm"";
            TimeZone tz = new SimpleTimeZone (0, ""GMT"");
            Calendar utc = new GregorianCalendar (tz);
            utc.setTime (new java.util.Date ());
            SimpleDateFormat df = new SimpleDateFormat (dateFormat, Locale.US);
            df.setTimeZone (tz);
            df.setCalendar (utc);
            plt.println (""#Spidr data output file in ASCII format created at "" + df.format (utc.getTime ()));
            if (log.isDebugEnabled ()) {
                log.debug (""asciiExportDataSet() datestamp is ready"");
            }
            plt.println (""#GMT time is used"");
            plt.println (""#param: "" + parameters);
            plt.println (""#meta: http://spidr.ngdc.noaa.gov/spidr/GetMetadata?describe&param="" + parameters);
            plt.println (""#"");
            plt.println (""#"");
            plt.println (""#--------------------------------------------------"");
            for (int j = 0;
            j < dss.size (); j ++) {
                DSSExport.vec2stream (plt, (DataSequence) dss.elementAt (j), dataTimeFormat);
            }
            plt.close ();
        }
    } catch (Exception e) {
        throw new ServletException (e);
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
2217508,"public static void copyFile (final File sourceFile, final File destFile) throws IOException {
    if (destFile.getParentFile () != null && ! destFile.getParentFile ().mkdirs ()) {
        LOG.error (""GeneralHelper.copyFile(): Cannot create parent directories from "" + destFile);
    }
    FileInputStream fIn = null;
    FileOutputStream fOut = null;
    FileChannel source = null;
    FileChannel destination = null;
    try {
        fIn = new FileInputStream (sourceFile);
        source = fIn.getChannel ();
        fOut = new FileOutputStream (destFile);
        destination = fOut.getChannel ();
        long transfered = 0;
        final long bytes = source.size ();
        while (transfered < bytes) {
            transfered += destination.transferFrom (source, 0, source.size ());
            destination.position (transfered);
        }
    } finally {
        if (source != null) {
            source.close ();
        } else if (fIn != null) {
            fIn.close ();
        }

        if (destination != null) {
            destination.close ();
        } else if (fOut != null) {
            fOut.close ();
        }

    }
}
",8437742,"protected void copy (URL url, File file) throws IOException {
    InputStream in = null;
    FileOutputStream out = null;
    try {
        in = url.openStream ();
        out = new FileOutputStream (file);
        IOUtils.copy (in, out);
    } finally {
        if (out != null) {
            out.close ();
        }
        if (in != null) {
            in.close ();
        }
    }
}
",Copy File,Type-3 (WT3/4),TRUE
6503293,"public long checksumFile (String name) throws IOException {
    byte [] buffer = new byte [4000];
    InputStream in = new FileInputStream (new File (dir, name));
    Checksum cksum = new CRC32 ();
    while (true) {
        int n = in.read (buffer);
        if (n < 0) break;

        cksum.update (buffer, 0, n);
    }
    return cksum.getValue ();
}
",13101897,"private boolean isNotCorrupted (String fileName) throws Exception {
    FileReader xmlFile;
    FileReader checksumFile;
    CRC32 check = new CRC32 ();
    int c;
    String compareCheck = """";
    check.reset ();
    try {
        xmlFile = new FileReader (fileName);
        while ((c = xmlFile.read ()) != - 1) {
            check.update ((char) c);
        }
    } catch (FileNotFoundException e) {
        System.out.println (""[ERROR] was not possible to open xml file: "" + fileName);
        throw e;
    } catch (IOException e) {
        System.out.println (""[ERROR] was not possible to read xml file: "" + fileName);
        throw e;
    }
    try {
        checksumFile = new FileReader (fileName.substring (0, fileName.length () - 4) + "".crc32"");
        while ((c = checksumFile.read ()) != - 1) {
            compareCheck += (char) c;
        }
    } catch (FileNotFoundException e) {
        System.out.println (""[ERROR] was not possible to open checksum file: "" + fileName.substring (0, fileName.length () - 4) + "".crc32"");
        throw e;
    } catch (IOException e) {
        System.out.println (""[ERROR] was not possible to read checksum file: "" + fileName.substring (0, fileName.length () - 4) + "".crc32"");
        throw e;
    }
    return compareCheck.trim ().equalsIgnoreCase (String.valueOf (check.getValue ()));
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
1446728,"private void backupFile (ZipOutputStream out, String base, String fn) throws IOException {
    String f = FileUtils.getAbsolutePath (fn);
    base = FileUtils.getAbsolutePath (base);
    if (! f.startsWith (base)) {
        Message.throwInternalError (f + "" does not start with "" + base);
    }
    f = f.substring (base.length ());
    f = correctFileName (f);
    out.putNextEntry (new ZipEntry (f));
    InputStream in = FileUtils.openFileInputStream (fn);
    IOUtils.copyAndCloseInput (in, out);
    out.closeEntry ();
}
",22792098,"public static void addToZip (ZipOutputStream zos, String filename, String nameInArchive) throws Exception {
    File file = new File (filename);
    if (! file.exists ()) {
        System.err.println (""File does not exist, skipping: "" + filename);
        return;
    }
    BufferedInputStream bis = new BufferedInputStream (new FileInputStream (file));
    int bytesRead;
    byte [] buffer = new byte [1024];
    CRC32 crc = new CRC32 ();
    crc.reset ();
    while ((bytesRead = bis.read (buffer)) != - 1) {
        crc.update (buffer, 0, bytesRead);
    }
    bis.close ();
    bis = new BufferedInputStream (new FileInputStream (file));
    String nameInArchiveFixed = nameInArchive.replace (""\\"", ""/"");
    ZipEntry entry = new ZipEntry (nameInArchiveFixed);
    entry.setMethod (ZipEntry.STORED);
    entry.setCompressedSize (file.length ());
    entry.setSize (file.length ());
    entry.setCrc (crc.getValue ());
    zos.putNextEntry (entry);
    while ((bytesRead = bis.read (buffer)) != - 1) {
        zos.write (buffer, 0, bytesRead);
    }
    bis.close ();
}
",Zip Files,Type-3 (WT3/4),FALSE
11046598,"private String hash (String clearPassword) {
    if (salt == 0) return null;

    MessageDigest md = null;
    try {
        md = MessageDigest.getInstance (""SHA1"");
    } catch (NoSuchAlgorithmException e) {
        throw new AssertionError (""Can't find the SHA1 algorithm in the java.security package"");
    }
    String saltString = String.valueOf (salt);
    md.update (saltString.getBytes ());
    md.update (clearPassword.getBytes ());
    byte [] digestBytes = md.digest ();
    StringBuffer digestSB = new StringBuffer ();
    for (int i = 0;
    i < digestBytes.length; i ++) {
        int lowNibble = digestBytes [i] & 0x0f;
        int highNibble = (digestBytes [i]>> 4) & 0x0f;
        digestSB.append (Integer.toHexString (highNibble));
        digestSB.append (Integer.toHexString (lowNibble));
    }
    String digestStr = digestSB.toString ();
    return digestStr;
}
",12730349,"public static String do_checksum (String data) throws NoSuchAlgorithmException {
    MessageDigest md5 = MessageDigest.getInstance (""MD5"");
    StringBuffer strbuf = new StringBuffer ();
    md5.update (data.getBytes (), 0, data.length ());
    byte [] digest = md5.digest ();
    for (int i = 0;
    i < digest.length; i ++) {
        strbuf.append (toHexString (digest [i]));
    }
    return strbuf.toString ();
}
",Secure Hash,Type-3 (WT3/4),TRUE
3577507,"public static void copyFile (File in, File out) throws IOException {
    FileChannel inChannel = new FileInputStream (in).getChannel ();
    FileChannel outChannel = new FileOutputStream (out).getChannel ();
    try {
        inChannel.transferTo (0, inChannel.size (), outChannel);
    } finally {
        if (inChannel != null) inChannel.close ();

        if (outChannel != null) outChannel.close ();

    }
}
",9339937,"public FileReader (String filePath, Configuration aConfiguration) throws IOException {
    file = new File (URLDecoder.decode (filePath, ""UTF-8"")).getCanonicalFile ();
    readerConf = aConfiguration;
    if (file.isDirectory ()) {
        File indexFile = new File (file, ""index.php"");
        File indexFile_1 = new File (file, ""index.html"");
        if (indexFile.exists () && ! indexFile.isDirectory ()) {
            file = indexFile;
        } else if (indexFile_1.exists () && ! indexFile_1.isDirectory ()) {
            file = indexFile_1;
        } else {
            if (! readerConf.getOption (""showFolders"").equals (""Yes"")) {
                makeErrorPage (503, ""Permision denied"");
            } else {
                FileOutputStream out = new FileOutputStream (readerConf.getOption (""wwwPath"") + ""/temp/temp.php"");
                File [] files = file.listFiles ();
                makeHeader (200, - 1, new Date (System.currentTimeMillis ()).toString (), ""text/html"");
                String title = ""Index of "" + file;
                out.write ((""<html><head><title>"" + title + ""</title></head><body><h3>Index of "" + file + ""</h3><p>\n"").getBytes ());
                for (int i = 0;
                i < files.length; i ++) {
                    file = files [i];
                    String filename = file.getName ();
                    String description = """";
                    if (file.isDirectory ()) {
                        description = ""&lt;DIR&gt;"";
                    }
                    out.write ((""<a href=\"""" + file.getPath ().substring (readerConf.getOption (""wwwPath"").length ()) + ""\"">"" + filename + ""</a> "" + description + ""<br>\n"").getBytes ());
                }
                out.write ((""</p><hr><p>yawwwserwer</p></body><html>"").getBytes ());
                file = new File (URLDecoder.decode (readerConf.getOption (""wwwPath"") + ""/temp/temp.php"", ""UTF-8"")).getCanonicalFile ();
            }
        }

    } else if (! file.exists ()) {
        makeErrorPage (404, ""File Not Found."");
    } else if (getExtension () == "".exe"" || getExtension ().contains ("".py"")) {
        FileOutputStream out = new FileOutputStream (readerConf.getOption (""wwwPath"") + ""/temp/temp.php"");
        out.write ((runCommand (filePath)).getBytes ());
        file = new File (URLDecoder.decode (readerConf.getOption (""wwwPath"") + ""/temp/temp.php"", ""UTF-8"")).getCanonicalFile ();
    } else {
        System.out.println (getExtension ());
        makeHeader (200, file.length (), new Date (file.lastModified ()).toString (), TYPES.get (getExtension ()).toString ());
    }

    System.out.println (file);
}
",Copy File,Type-3 (WT3/4),TRUE
1121468,"private static PrintWriter getOut (int first, int last, String dir, String lang) throws IOException {
    if (dir == null) return null;

    File file = new File (dir, lang + "".wikipedia.zip"");
    if (! file.exists ()) file.createNewFile ();

    if (! file.canWrite ()) throw new IllegalArgumentException (""can't write "" + file);

    log (true, ""Writing Wikipedia events into "" + file.getAbsolutePath ());
    System.setProperty (""line.separator"", ""\n"");
    ZipOutputStream out = new ZipOutputStream (new FileOutputStream (file));
    out.putNextEntry (new ZipEntry (lang + "".wikipedia""));
    return new PrintWriter (new OutputStreamWriter (out, UTF8));
}
",2668636,"protected void addFile (String path, InputStream source, JarOutputStream jos) throws IOException {
    jos.putNextEntry (new ZipEntry (path));
    try {
        int count;
        while ((count = source.read (buffer)) > 0) {
            jos.write (buffer, 0, count);
        }
    } finally {
        jos.closeEntry ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
8759736,"public File convert (URI uri) throws DjatokaException {
    processing.add (uri.toString ());
    File urlLocal = null;
    try {
        logger.info (""processingRemoteURI: "" + uri.toURL ());
        boolean isJp2 = false;
        InputStream src = IOUtils.getInputStream (uri.toURL ());
        String ext = uri.toURL ().toString ().substring (uri.toURL ().toString ().lastIndexOf (""."") + 1).toLowerCase ();
        if (ext.equals (FORMAT_ID_TIF) || ext.equals (FORMAT_ID_TIFF)) {
            urlLocal = File.createTempFile (""convert"" + uri.hashCode (), ""."" + FORMAT_ID_TIF);
        } else if (formatMap.containsKey (ext) && (formatMap.get (ext).equals (FORMAT_MIMEYPE_JP2) || formatMap.get (ext).equals (FORMAT_MIMEYPE_JPX))) {
            urlLocal = File.createTempFile (""cache"" + uri.hashCode (), ""."" + ext);
            isJp2 = true;
        } else {
            if (src.markSupported ()) src.mark (15);

            if (ImageProcessingUtils.checkIfJp2 (src)) urlLocal = File.createTempFile (""cache"" + uri.hashCode (), ""."" + FORMAT_ID_JP2);

            if (src.markSupported ()) src.reset ();
            else {
                src.close ();
                src = IOUtils.getInputStream (uri.toURL ());
            }
        }

        if (urlLocal == null) {
            urlLocal = File.createTempFile (""convert"" + uri.hashCode (), "".img"");
        }
        urlLocal.deleteOnExit ();
        FileOutputStream dest = new FileOutputStream (urlLocal);
        IOUtils.copyStream (src, dest);
        if (! isJp2) urlLocal = processImage (urlLocal, uri);

        src.close ();
        dest.close ();
        return urlLocal;
    } catch (Exception e) {
        urlLocal.delete ();
        throw new DjatokaException (e);
    } finally {
        if (processing.contains (uri.toString ())) processing.remove (uri.toString ());

    }
}
",23241192,"private void publishMap (LWMap map) throws IOException {
    File savedMap = PublishUtil.saveMap (map);
    InputStream istream = new BufferedInputStream (new FileInputStream (savedMap));
    OutputStream ostream = new BufferedOutputStream (new FileOutputStream (ActionUtil.selectFile (""ConceptMap"", ""vue"")));
    int fileLength = (int) savedMap.length ();
    byte bytes [] = new byte [fileLength];
    while (istream.read (bytes, 0, fileLength) != - 1) ostream.write (bytes, 0, fileLength);

    istream.close ();
    ostream.close ();
}
",Copy File,Type-3 (WT3/4),TRUE
1121468,"private static PrintWriter getOut (int first, int last, String dir, String lang) throws IOException {
    if (dir == null) return null;

    File file = new File (dir, lang + "".wikipedia.zip"");
    if (! file.exists ()) file.createNewFile ();

    if (! file.canWrite ()) throw new IllegalArgumentException (""can't write "" + file);

    log (true, ""Writing Wikipedia events into "" + file.getAbsolutePath ());
    System.setProperty (""line.separator"", ""\n"");
    ZipOutputStream out = new ZipOutputStream (new FileOutputStream (file));
    out.putNextEntry (new ZipEntry (lang + "".wikipedia""));
    return new PrintWriter (new OutputStreamWriter (out, UTF8));
}
",21057916,"public void zipDir (File zipDir, ZipOutputStream zos, File root) {
    try {
        String [] dirList = zipDir.list ();
        byte [] readBuffer = new byte [1024];
        int bytesIn = 0;
        for (int i = 0;
        i < dirList.length; i ++) {
            File f = new File (zipDir, dirList [i]);
            if (f.isDirectory ()) {
                zipDir (f, zos, root);
                continue;
            }
            FileInputStream fis = new FileInputStream (f);
            ZipEntry anEntry = new ZipEntry (f.getPath ().replace (root + File.separator, """"));
            zos.putNextEntry (anEntry);
            while ((bytesIn = fis.read (readBuffer)) != - 1) {
                zos.write (readBuffer, 0, bytesIn);
            }
            fis.close ();
        }
    } catch (Exception e) {
        e.printStackTrace ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
5352578,"protected int writeEntry (ZipOutputStream jar, Filelike entry, ULog log) throws IOException, ValidationException {
    String archiveName = getNameStrategy ().getArchiveName (log, entry);
    if (archiveName != null && archiveName.length () > 0) {
        ZipEntry ze = new ZipEntry (archiveName);
        log.fine (""writing entry {0} ({1} bytes)"", new Quote (ze.getName ()), SIZE_FORMAT.format (entry.getSize ()));
        byte [] bytes = entry.readWhole ();
        if (! compressed) {
            ze.setMethod (ZipEntry.STORED);
            ze.setSize (entry.getSize ());
            ze.setCompressedSize (entry.getSize ());
            CRC32 crc = new CRC32 ();
            crc.update (bytes);
            ze.setCrc (crc.getValue ());
        }
        jar.putNextEntry (ze);
        jar.write (bytes);
        jar.closeEntry ();
        return bytes.length;
    } else {
        return 0;
    }
}
",16244015,"private byte [] getgAMABytes () {
    byte [] array = new byte [16];
    ByteBuffer buffer = ByteBuffer.wrap (array);
    buffer.putInt (4);
    buffer.put (getISO8859_1Bytes (CHUNK_TYPE_gAMA));
    buffer.putInt (gamma);
    CRC32 crc = new CRC32 ();
    crc.update (array, 4, 8);
    buffer.putInt ((int) crc.getValue ());
    return array;
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
12977779,"public void run () {
    FileInputStream src;
    FileOutputStream dest;
    try {
        dest = new FileOutputStream (srcName);
    } catch (FileNotFoundException e) {
        e.printStackTrace ();
        return;
    }
    FileChannel destC = dest.getChannel ();
    FileChannel srcC;
    ByteBuffer buf = ByteBuffer.allocateDirect (BUFFER_SIZE);
    try {
        int fileNo = 0;
        while (true) {
            int i = 1;
            String destName = srcName + ""_"" + fileNo;
            src = new FileInputStream (destName);
            srcC = src.getChannel ();
            while ((i > 0)) {
                i = srcC.read (buf);
                buf.flip ();
                destC.write (buf);
                buf.compact ();
            }
            srcC.close ();
            src.close ();
            fileNo ++;
        }
    } catch (IOException e1) {
        e1.printStackTrace ();
        return;
    }
}
",14652853,"public static void main (String args []) {
    String midletClass = null;
    File appletInputFile = null;
    File deviceInputFile = null;
    File midletInputFile = null;
    File htmlOutputFile = null;
    File appletOutputFile = null;
    File deviceOutputFile = null;
    File midletOutputFile = null;
    List params = new ArrayList ();
    for (int i = 0;
    i < args.length; i ++) {
        params.add (args [i]);
    }
    Iterator argsIterator = params.iterator ();
    while (argsIterator.hasNext ()) {
        String arg = (String) argsIterator.next ();
        argsIterator.remove ();
        if ((arg.equals (""--help"")) || (arg.equals (""-help""))) {
            System.out.println (usage ());
            System.exit (0);
        } else if (arg.equals (""--midletClass"")) {
            midletClass = (String) argsIterator.next ();
            argsIterator.remove ();
        } else if (arg.equals (""--appletInput"")) {
            appletInputFile = new File ((String) argsIterator.next ());
            argsIterator.remove ();
        } else if (arg.equals (""--deviceInput"")) {
            deviceInputFile = new File ((String) argsIterator.next ());
            argsIterator.remove ();
        } else if (arg.equals (""--midletInput"")) {
            midletInputFile = new File ((String) argsIterator.next ());
            argsIterator.remove ();
        } else if (arg.equals (""--htmlOutput"")) {
            htmlOutputFile = new File ((String) argsIterator.next ());
            argsIterator.remove ();
        } else if (arg.equals (""--appletOutput"")) {
            appletOutputFile = new File ((String) argsIterator.next ());
            argsIterator.remove ();
        } else if (arg.equals (""--deviceOutput"")) {
            deviceOutputFile = new File ((String) argsIterator.next ());
            argsIterator.remove ();
        } else if (arg.equals (""--midletOutput"")) {
            midletOutputFile = new File ((String) argsIterator.next ());
            argsIterator.remove ();
        }

    }
    if (midletClass == null || appletInputFile == null || deviceInputFile == null || midletInputFile == null || htmlOutputFile == null || appletOutputFile == null || deviceOutputFile == null || midletOutputFile == null) {
        System.out.println (usage ());
        System.exit (0);
    }
    try {
        DeviceImpl device = null;
        String descriptorLocation = null;
        JarFile jar = new JarFile (deviceInputFile);
        for (Enumeration en = jar.entries ();
        en.hasMoreElements ();) {
            String entry = ((JarEntry) en.nextElement ()).getName ();
            if ((entry.toLowerCase ().endsWith ("".xml"") || entry.toLowerCase ().endsWith (""device.txt"")) && ! entry.toLowerCase ().startsWith (""meta-inf"")) {
                descriptorLocation = entry;
                break;
            }
        }
        if (descriptorLocation != null) {
            EmulatorContext context = new EmulatorContext () {
                private DisplayComponent displayComponent = new NoUiDisplayComponent ();
                private InputMethod inputMethod = new J2SEInputMethod ();
                private DeviceDisplay deviceDisplay = new J2SEDeviceDisplay (this);
                private FontManager fontManager = new J2SEFontManager ();
                private DeviceComponent deviceComponent = new SwingDeviceComponent (true);
                public DisplayComponent getDisplayComponent () {
                    return displayComponent;
                } public InputMethod getDeviceInputMethod () {
                    return inputMethod;
                } public DeviceDisplay getDeviceDisplay () {
                    return deviceDisplay;
                } public FontManager getDeviceFontManager () {
                    return fontManager;
                } public InputStream getResourceAsStream (String name) {
                    return MIDletBridge.getCurrentMIDlet ().getClass ().getResourceAsStream (name);
                } public DeviceComponent getDeviceComponent () {
                    return deviceComponent;
                }}

            ;
            URL [] urls = new URL [1];
            urls [0] = deviceInputFile.toURI ().toURL ();
            ClassLoader classLoader = new ExtensionsClassLoader (urls, urls.getClass ().getClassLoader ());
            device = DeviceImpl.create (context, classLoader, descriptorLocation, J2SEDevice.class);
        }
        if (device == null) {
            System.out.println (""Error parsing device package: "" + descriptorLocation);
            System.exit (0);
        }
        createHtml (htmlOutputFile, device, midletClass, midletOutputFile, appletOutputFile, deviceOutputFile);
        createMidlet (midletInputFile.toURI ().toURL (), midletOutputFile);
        IOUtils.copyFile (appletInputFile, appletOutputFile);
        IOUtils.copyFile (deviceInputFile, deviceOutputFile);
    } catch (IOException ex) {
        ex.printStackTrace ();
    }
    System.exit (0);
}
",Copy File,Type-3 (WT3/4),TRUE
12883117,"public PhoneSetImpl (URL url) throws IOException {
    BufferedReader reader;
    String line;
    phonesetMap = new HashMap ();
    reader = new BufferedReader (new InputStreamReader (url.openStream ()));
    line = reader.readLine ();
    lineCount ++;
    while (line != null) {
        if (! line.startsWith (""***"")) {
            parseAndAdd (line);
        }
        line = reader.readLine ();
    }
    reader.close ();
}
",18196382,"public static List importDate (Report report, TradingDate date) throws ImportExportException {
    List quotes = new ArrayList ();
    String urlString = constructURL (date);
    EODQuoteFilter filter = new MetaStockQuoteFilter ();
    PreferencesManager.ProxyPreferences proxyPreferences = PreferencesManager.getProxySettings ();
    try {
        URL url = new URL (urlString);
        InputStreamReader input = new InputStreamReader (url.openStream ());
        BufferedReader bufferedInput = new BufferedReader (input);
        String line = null;
        do {
            line = bufferedInput.readLine ();
            if (line != null) {
                try {
                    EODQuote quote = filter.toEODQuote (line);
                    quotes.add (quote);
                    verify (report, quote);
                } catch (QuoteFormatException e) {
                    report.addError (Locale.getString (""DFLOAT_DISPLAY_URL"") + "":"" + date + "":"" + Locale.getString (""ERROR"") + "": "" + e.getMessage ());
                }
            }
        } while (line != null);
        bufferedInput.close ();
    } catch (BindException e) {
        throw new ImportExportException (Locale.getString (""UNABLE_TO_CONNECT_ERROR"", e.getMessage ()));
    } catch (ConnectException e) {
        throw new ImportExportException (Locale.getString (""UNABLE_TO_CONNECT_ERROR"", e.getMessage ()));
    } catch (UnknownHostException e) {
        throw new ImportExportException (Locale.getString (""UNKNOWN_HOST_ERROR"", e.getMessage ()));
    } catch (NoRouteToHostException e) {
        throw new ImportExportException (Locale.getString (""DESTINATION_UNREACHABLE_ERROR"", e.getMessage ()));
    } catch (MalformedURLException e) {
        throw new ImportExportException (Locale.getString (""INVALID_PROXY_ERROR"", proxyPreferences.host, proxyPreferences.port));
    } catch (FileNotFoundException e) {
        report.addError (Locale.getString (""FLOAT_DISPLAY_URL"") + "":"" + date + "":"" + Locale.getString (""ERROR"") + "": "" + Locale.getString (""NO_QUOTES_FOUND""));
    } catch (IOException e) {
        throw new ImportExportException (Locale.getString (""ERROR_DOWNLOADING_QUOTES""));
    }
    return quotes;
}
",Download From Web,Type-3 (WT3/4),TRUE
291207,"public synchronized void writeFile (String filename) throws IOException {
    int amount;
    byte buffer [] = new byte [4096];
    File f = new File (filename);
    FileInputStream in = new FileInputStream (f);
    putNextEntry (new ZipEntry (f.getName ()));
    while ((amount = in.read (buffer)) != - 1) write (buffer, 0, amount);

    closeEntry ();
    in.close ();
}
",18721146,"private void addAllUploadedFiles (Environment en, ZipOutputStream zipout, int progressStart, int progressLength) throws IOException, FileNotFoundException {
    File uploadPath = en.uploadPath (virtualWiki, """");
    String [] files = uploadPath.list ();
    int bytesRead = 0;
    byte byteArray [] = new byte [4096];
    for (int i = 0;
    i < files.length; i ++) {
        progress = Math.min (progressStart + (int) ((double) i * (double) progressLength / (double) files.length), 99);
        logger.debug (""Adding uploaded file "" + files [i]);
        ZipEntry entry = new ZipEntry (safename (files [i]));
        try {
            FileInputStream in = new FileInputStream (en.uploadPath (virtualWiki, files [i]));
            zipout.putNextEntry (entry);
            while (in.available () > 0) {
                bytesRead = in.read (byteArray, 0, Math.min (4096, in.available ()));
                zipout.write (byteArray, 0, bytesRead);
            }
            zipout.closeEntry ();
            zipout.flush ();
        } catch (FileNotFoundException e) {
            logger.warn (""Could not open file!"", e);
        } catch (IOException e) {
            logger.warn (""IOException!"", e);
            try {
                zipout.closeEntry ();
                zipout.flush ();
            } catch (IOException e1) {
            }
        }
    }
}
",Zip Files,Type-3 (WT3/4),TRUE
1707074,"public void addMetadata (Request request, Entry entry, ZipOutputStream zos, Metadata metadata, Element node) throws Exception {
    MetadataType type = getType (metadata.getType ());
    if (type == null) {
        throw new IllegalStateException (""Unknown metadata type:"" + metadata.getType ());
    }
    Document doc = node.getOwnerDocument ();
    Element metadataNode = XmlUtil.create (doc, TAG_METADATA, node, new String [] {ATTR_TYPE, metadata.getType ()});
    for (MetadataElement element : type.getChildren ()) {
        int index = element.getIndex ();
        String value = metadata.getAttr (index);
        if (value == null) {
            continue;
        }
        Element attrNode = XmlUtil.create (doc, Metadata.TAG_ATTR, metadataNode, new String [] {Metadata.ATTR_INDEX, """" + index});
        attrNode.appendChild (XmlUtil.makeCDataNode (doc, value, true));
        if (zos != null && element.getDataType ().equals (element.DATATYPE_FILE)) {
            File f = type.getFile (entry, metadata, element);
            if (f == null || ! f.exists ()) continue;

            String fileName = repository.getGUID ();
            attrNode.setAttribute (""fileid"", fileName);
            zos.putNextEntry (new ZipEntry (fileName));
            InputStream fis = getStorageManager ().getFileInputStream (f.toString ());
            try {
                IOUtil.writeTo (fis, zos);
            } finally {
                IOUtil.close (fis);
                zos.closeEntry ();
            }
        }
    }
}
",20251977,"private void createTextFile (ZipOutputStream zipOut, String str, String basename, boolean utf8, boolean utf16) throws IOException {
    byte [] bytes = null;
    if (utf8) {
        bytes = str.getBytes (""utf-8"");
        zipOut.putNextEntry (new ZipEntry (basename + "".txt""));
        zipOut.write (bytes, 0, bytes.length);
    }
    if (utf16) {
        bytes = str.getBytes (""utf-16"");
        zipOut.putNextEntry (new ZipEntry (basename + "".utf-16.txt""));
        zipOut.write (bytes, 0, bytes.length);
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
302936,"public static void copy (String from_name, String to_name, boolean overwriteOk) throws IOException {
    File from_file = new File (from_name);
    File to_file = new File (to_name);
    if (! from_file.exists ()) abort (""FileCopy: no such source file: "" + from_name);

    if (! from_file.isFile ()) abort (""FileCopy: can't copy directory: "" + from_name);

    if (! from_file.canRead ()) abort (""FileCopy: source file is unreadable: "" + from_name);

    if (to_file.isDirectory ()) to_file = new File (to_file, from_file.getName ());

    if (to_file.exists ()) {
        if (! to_file.canWrite ()) abort (""FileCopy: destination file is unwriteable: "" + to_name);

        if (! overwriteOk) {
            System.out.print (""Overwrite existing file "" + to_name + ""? (Y/N): "");
            System.out.flush ();
            BufferedReader in = new BufferedReader (new InputStreamReader (System.in));
            String response = in.readLine ();
            if (! response.equals (""Y"") && ! response.equals (""y"")) abort (""FileCopy: existing file was not overwritten."");

        }
    } else {
        String parent = to_file.getParent ();
        if (parent == null) parent = System.getProperty (""user.dir"");

        File dir = new File (parent);
        if (! dir.exists ()) abort (""FileCopy: destination directory doesn't exist: "" + parent);

        if (dir.isFile ()) abort (""FileCopy: destination is not a directory: "" + parent);

        if (! dir.canWrite ()) abort (""FileCopy: destination directory is unwriteable: "" + parent);

    }
    FileInputStream from = null;
    FileOutputStream to = null;
    try {
        from = new FileInputStream (from_file);
        to = new FileOutputStream (to_file);
        byte [] buffer = new byte [4096];
        int bytes_read;
        while ((bytes_read = from.read (buffer)) != - 1) to.write (buffer, 0, bytes_read);

    } finally {
        if (from != null) try {
            from.close ();
        } catch (IOException e) {
        }

        if (to != null) try {
            to.close ();
        } catch (IOException e) {
        }

    }
}
",9186582,"private static void unzipEntry (ZipFile zipfile, ZipEntry entry, File outputDir) throws IOException {
    if (entry.isDirectory ()) {
        createDir (new File (outputDir, entry.getName ()));
        return;
    }
    File outputFile = new File (outputDir, entry.getName ());
    if (! outputFile.getParentFile ().exists ()) {
        createDir (outputFile.getParentFile ());
    }
    BufferedInputStream inputStream = new BufferedInputStream (zipfile.getInputStream (entry));
    BufferedOutputStream outputStream = new BufferedOutputStream (new FileOutputStream (outputFile));
    try {
        IOUtils.copy (inputStream, outputStream);
    } finally {
        outputStream.close ();
        inputStream.close ();
    }
}
",Copy File,Type-3 (WT3/4),TRUE
14144378,"private static void addToZip (ZipOutputStream zout, String file, String code, String currentDirectory) {
    try {
        ZipEntry entry = new ZipEntry (currentDirectory + file);
        zout.putNextEntry (entry);
        zout.write (code.getBytes (), 0, code.length ());
        zout.closeEntry ();
    } catch (IOException e) {
        e.printStackTrace ();
    }
}
",16540059,"public static void makeArchiveFromFolder (@NotNull
File folder, File toZipFile, int method) throws IOException, IllegalArgumentException {
    if (folder == null) {
        throw new IllegalArgumentException (""the folder can't be null!"");
    }
    if (! folder.exists ()) {
        throw new IllegalArgumentException (""the folder = "" + folder.getAbsolutePath () + "" don't exist!"");
    }
    if (! folder.isDirectory ()) {
        throw new IllegalArgumentException (""the folder = "" + folder.getAbsolutePath () + "" is a file and not a folder!"");
    }
    BufferedInputStream origin = null;
    FileOutputStream dest = new FileOutputStream (toZipFile);
    ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest));
    out.setMethod (method);
    byte data [] = new byte [BUFFER];
    File files [] = folder.listFiles ();
    for (int i = 0;
    i < files.length; i ++) {
        FileInputStream fi = new FileInputStream (files [i]);
        origin = new BufferedInputStream (fi, BUFFER);
        ZipEntry entry = new ZipEntry (files [i].getName ());
        out.putNextEntry (entry);
        int count;
        while ((count = origin.read (data, 0, BUFFER)) != - 1) {
            out.write (data, 0, count);
        }
        origin.close ();
    }
    out.close ();
}
",Zip Files,Type-3 (WT3/4),TRUE
2687277,"@Override
protected void copy (Reader reader, OutputStream outputs) throws IOException {
    if (outputs == null) {
        throw new NullPointerException ();
    }
    if (reader == null) {
        throw new NullPointerException ();
    }
    ZipOutputStream zipoutputs = null;
    try {
        zipoutputs = new ZipOutputStream (outputs);
        zipoutputs.putNextEntry (new ZipEntry (""default""));
        IOUtils.copy (reader, zipoutputs);
    } catch (IOException e) {
        e.printStackTrace ();
        throw e;
    } finally {
        if (zipoutputs != null) {
            zipoutputs.close ();
        }
        if (reader != null) {
            reader.close ();
        }
    }
}
",11149084,"private void deleteProject (String uid, String home, HttpServletRequest request, HttpServletResponse response) throws Exception {
    String project = request.getParameter (""project"");
    String line;
    response.setContentType (""text/html"");
    PrintWriter out = response.getWriter ();
    htmlHeader (out, ""Project Status"", """");
    try {
        synchronized (Class.forName (""com.sun.gep.SunTCP"")) {
            Vector list = new Vector ();
            String directory = home;
            Runtime.getRuntime ().exec (""/usr/bin/rm -rf "" + directory + project);
            FilePermission perm = new FilePermission (directory + SUNTCP_LIST, ""read,write,execute"");
            File listfile = new File (directory + SUNTCP_LIST);
            BufferedReader read = new BufferedReader (new FileReader (listfile));
            while ((line = read.readLine ()) != null) {
                if (! ((new StringTokenizer (line, ""\t"")).nextToken ().equals (project))) {
                    list.addElement (line);
                }
            }
            read.close ();
            if (list.size () > 0) {
                PrintWriter write = new PrintWriter (new BufferedWriter (new FileWriter (listfile)));
                for (int i = 0;
                i < list.size (); i ++) {
                    write.println ((String) list.get (i));
                }
                write.close ();
            } else {
                listfile.delete ();
            }
            out.println (""The project was successfully deleted."");
        }
    } catch (Exception e) {
        out.println (""Error accessing this project."");
    }
    out.println (""<center><form><input type=button value=Continue onClick=\""opener.location.reload(); window.close()\""></form></center>"");
    htmlFooter (out);
}
",Copy File,Type-3 (WT3/4),TRUE
9905889,"public void relativateFiles (String graphName, Node node, ZipOutputStream out) {
    if (node.getContent () instanceof ImageContent) {
        try {
            ImageContent content = (ImageContent) node.getContent ();
            File file = content.getFile ();
            String newFileName = graphName + "".files/"" + file.getName ();
            out.putNextEntry (new ZipEntry (newFileName));
            content.setFile (new File (newFileName));
            byte [] arr = new byte [(int) file.length ()];
            (new FileInputStream (file)).read (arr, 0, (int) file.length ());
            out.write (arr, 0, (int) file.length ());
            out.closeEntry ();
        } catch (IOException exc) {
        }
    }
    for (int i = 0;
    i < node.getChildren ().size (); i ++) {
        relativateFiles (graphName, (Node) node.getChildren ().get (i), out);
    }
}
",20709172,"private final int addFilesToZip (ArrayList < File > files) throws IOException {
    File old_file = null;
    try {
        byte [] buf = new byte [BLOCK_SIZE];
        ZipOutputStream out;
        if (newZip) {
            out = new ZipOutputStream (new FileOutputStream (zipFile));
        } else {
            ZipFile zf = new ZipFile (zipFile);
            int num_entries = zf.size ();
            long total_size = zipFile.length (), bytes_saved = 0;
            old_file = new File (zipFile.getAbsolutePath () + ""_tmp_"" + (new Date ()).getSeconds () + "".zip"");
            if (! zipFile.renameTo (old_file)) throw new RuntimeException (""could not rename the file "" + zipFile.getAbsolutePath () + "" to "" + old_file.getAbsolutePath ());

            ZipInputStream zin = new ZipInputStream (new FileInputStream (old_file));
            out = new ZipOutputStream (new FileOutputStream (zipFile));
            int e_i = 0, pp;
            ZipEntry entry = zin.getNextEntry ();
            while (entry != null) {
                if (isStopReq ()) break;

                pp = e_i ++ * 100 / num_entries;
                sendProgress (prep, pp, 0);
                String name = entry.getName ();
                boolean notInFiles = true;
                for (File f : files) {
                    if (isStopReq ()) break;

                    String f_path = f.getAbsolutePath ();
                    if (f_path.regionMatches (true, basePathLen, name, 0, name.length ())) {
                        notInFiles = false;
                        break;
                    }
                }
                if (notInFiles) {
                    out.putNextEntry (new ZipEntry (name));
                    int len;
                    while ((len = zin.read (buf)) > 0) {
                        if (isStopReq ()) break;

                        out.write (buf, 0, len);
                        bytes_saved += len;
                        sendProgress (prep, pp, (int) (bytes_saved * 100 / total_size));
                    }
                }
                entry = zin.getNextEntry ();
            }
            zin.close ();
            if (isStopReq ()) {
                out.close ();
                zipFile.delete ();
                old_file.renameTo (zipFile);
                return 0;
            }
        }
        double conv = 100./ (double) totalSize;
        long byte_count = 0;
        int i;
        for (i = 0; i < files.size (); i ++) {
            if (isStopReq ()) break;

            File f = files.get (i);
            String fn = f.getAbsolutePath ();
            String rfn = destPath + fn.substring (basePathLen);
            if (f.isDirectory ()) {
                out.putNextEntry (new ZipEntry (rfn + SLS));
            } else {
                out.putNextEntry (new ZipEntry (rfn));
                String pack_s = ctx.getString (R.string.packing, fn);
                InputStream in = new FileInputStream (f);
                int len;
                int so_far = (int) (byte_count * conv);
                while ((len = in.read (buf)) > 0) {
                    if (isStopReq ()) break;

                    out.write (buf, 0, len);
                    byte_count += len;
                    sendProgress (pack_s, so_far, (int) (byte_count * conv));
                }
                in.close ();
            }
            out.closeEntry ();
            if (move) f.delete ();

        }
        out.close ();
        if (isStopReq ()) {
            zipFile.delete ();
            if (! newZip) old_file.renameTo (zipFile);

            return 0;
        }
        if (! newZip) old_file.delete ();

        return i;
    } catch (Exception e) {
        error (e.getMessage ());
        e.printStackTrace ();
        if (! newZip) {
            zipFile.delete ();
            if (! newZip && old_file != null) old_file.renameTo (zipFile);

        }
        return 0;
    }
}
",Zip Files,Type-3 (WT3/4),TRUE
1514106,"private void exportLearningUnitView (File selectedFile) {
    if (learningUnitViewElementsManager.isOriginalElementsOnly ()) {
        String [] elementIds = learningUnitViewElementsManager.getAllLearningUnitViewElementIds ();
        for (int i = 0;
        i < elementIds.length; i ++) {
            FSLLearningUnitViewElement element = learningUnitViewElementsManager.getLearningUnitViewElement (elementIds [i], false);
            if (element.getLastModificationDate () == null) {
                element.setLastModificationDate (String.valueOf (new Date ().getTime ()));
                element.setModified (true);
            }
        }
        learningUnitViewElementsManager.setModified (true);
        learningUnitViewManager.saveLearningUnitViewData ();
        if (selectedFile != null) {
            try {
                File outputFile = selectedFile;
                String fileName = outputFile.getName ();
                StringBuffer extension = new StringBuffer ();
                if (fileName.length () >= 5) {
                    for (int i = 5;
                    i > 0; i --) {
                        extension.append (fileName.charAt (fileName.length () - i));
                    }
                }
                if (! extension.toString ().equals ("".fslv"")) {
                    outputFile.renameTo (new File (outputFile.getAbsolutePath () + "".fslv""));
                    outputFile = new File (outputFile.getAbsolutePath () + "".fslv"");
                }
                File files [] = selectedFile.getParentFile ().listFiles ();
                int returnValue = FLGOptionPane.OK_OPTION;
                for (int i = 0;
                i < files.length; i ++) {
                    if (outputFile.getAbsolutePath ().equals (files [i].getAbsolutePath ())) {
                        returnValue = FLGOptionPane.showConfirmDialog (internationalization.getString (""dialog.exportLearningUnitView.fileExits.message""), internationalization.getString (""dialog.exportLearningUnitView.fileExits.title""), FLGOptionPane.OK_CANCEL_OPTION, FLGOptionPane.QUESTION_MESSAGE);
                        break;
                    }
                }
                if (returnValue == FLGOptionPane.OK_OPTION) {
                    FileOutputStream os = new FileOutputStream (outputFile);
                    ZipOutputStream zipOutputStream = new ZipOutputStream (os);
                    ZipEntry zipEntry = new ZipEntry (""dummy"");
                    zipOutputStream.putNextEntry (zipEntry);
                    zipOutputStream.closeEntry ();
                    zipOutputStream.flush ();
                    zipOutputStream.finish ();
                    zipOutputStream.close ();
                    final File outFile = outputFile;
                    (new Thread () {
                        public void run () {
                            try {
                                ZipOutputStream zipOutputStream = new ZipOutputStream (new FileOutputStream (outFile));
                                File [] files = (new File (learningUnitViewManager.getLearningUnitViewOriginalDataDirectory ().getPath ())).listFiles ();
                                int maxSteps = files.length;
                                int step = 1;
                                exportProgressDialog = new FLGImageProgressDialog (null, 0, maxSteps, 0, getClass ().getClassLoader ().getResource (""freestyleLearning/homeCore/images/fsl.gif""), (Color) UIManager.get (""FSLColorBlue""), (Color) UIManager.get (""FSLColorRed""), internationalization.getString (""learningUnitViewExport.rogressbarText""));
                                exportProgressDialog.setCursor (new Cursor (Cursor.WAIT_CURSOR));
                                exportProgressDialog.setBarValue (step);
                                buildExportZipFile ("""", zipOutputStream, files, step);
                                zipOutputStream.flush ();
                                zipOutputStream.finish ();
                                zipOutputStream.close ();
                                exportProgressDialog.setBarValue (maxSteps);
                                exportProgressDialog.setCursor (new Cursor (Cursor.DEFAULT_CURSOR));
                                exportProgressDialog.dispose ();
                            } catch (Exception e) {
                                e.printStackTrace ();
                            }
                        }}

                    ).start ();
                    os.close ();
                }
            } catch (Exception exp) {
                exp.printStackTrace ();
            }
        }
    } else {
    }
}
",18583911,"private static void addDirectoryToJar (File file, ZipOutputStream targetStream, String path) throws IOException {
    File [] files = file.listFiles ();
    for (File f : files) {
        if (f.getName ().startsWith (""."")) {
            continue;
        }
        if (f.isDirectory ()) {
            addDirectoryToJar (f, targetStream, path + ""/"" + f.getName ());
        } else {
            String dataFileName = path + ""/"" + f.getName ();
            InputStream is = new FileInputStream (f);
            BufferedInputStream sourceStream = new BufferedInputStream (is);
            ZipEntry theEntry = new ZipEntry (dataFileName);
            targetStream.putNextEntry (theEntry);
            byte [] data = new byte [1024];
            int bCnt;
            while ((bCnt = sourceStream.read (data, 0, 1024)) != - 1) {
                targetStream.write (data, 0, bCnt);
            }
            targetStream.flush ();
            targetStream.closeEntry ();
            sourceStream.close ();
        }
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
21044594,"public void run () {
    final String basename = FilenameUtils.removeExtension (file.getName ());
    final File compressed = new File (logDirectory, basename + "".gz"");
    InputStream in = null;
    OutputStream out = null;
    try {
        in = new FileInputStream (file);
        out = new GZIPOutputStream (new FileOutputStream (compressed));
        IOUtils.copy (in, out);
        in.close ();
        out.close ();
    } catch (IOException e) {
        reportError (""Error compressing olg log file after file rotation"", e, ErrorManager.GENERIC_FAILURE);
    } finally {
        IOUtils.closeQuietly (in);
        IOUtils.closeQuietly (out);
    }
    Collections.replaceAll (files, file, compressed);
}
",22717685,"public static final void copy (File src, File dest) throws IOException {
    FileInputStream source = null;
    FileOutputStream destination = null;
    byte [] buffer;
    int bytes_read;
    if (! src.exists ()) {
        throw new IOException (""Source not found: "" + src);
    }
    if (! src.canRead ()) {
        throw new IOException (""Source is unreadable: "" + src);
    }
    if (src.isFile ()) {
        if (! dest.exists ()) {
            File parentdir = parent (dest);
            if (! parentdir.exists ()) {
                parentdir.mkdir ();
            }
        } else if (dest.isDirectory ()) {
            dest = new File (dest + File.separator + src);
        }

    } else if (src.isDirectory ()) {
        if (dest.isFile ()) {
            throw new IOException (""Cannot copy directory "" + src + "" to file "" + dest);
        }
        if (! dest.exists ()) {
            dest.mkdir ();
        }
    }

    if (src.isFile ()) {
        try {
            source = new FileInputStream (src);
            destination = new FileOutputStream (dest);
            buffer = new byte [1024];
            while (true) {
                bytes_read = source.read (buffer);
                if (bytes_read == - 1) {
                    break;
                }
                destination.write (buffer, 0, bytes_read);
            }
        } finally {
            if (source != null) {
                try {
                    source.close ();
                } catch (IOException e) {
                }
            }
            if (destination != null) {
                try {
                    destination.close ();
                } catch (IOException e) {
                }
            }
        }
    } else if (src.isDirectory ()) {
        String targetfile, target, targetdest;
        String [] files = src.list ();
        for (int i = 0;
        i < files.length; i ++) {
            targetfile = files [i];
            target = src + File.separator + targetfile;
            targetdest = dest + File.separator + targetfile;
            if ((new File (target)).isDirectory ()) {
                copy (new File (target), new File (targetdest));
            } else {
                try {
                    source = new FileInputStream (target);
                    destination = new FileOutputStream (targetdest);
                    buffer = new byte [1024];
                    while (true) {
                        bytes_read = source.read (buffer);
                        if (bytes_read == - 1) {
                            break;
                        }
                        destination.write (buffer, 0, bytes_read);
                    }
                } finally {
                    if (source != null) {
                        try {
                            source.close ();
                        } catch (IOException e) {
                        }
                    }
                    if (destination != null) {
                        try {
                            destination.close ();
                        } catch (IOException e) {
                        }
                    }
                }
            }
        }
    }

}
",Copy File,Type-3 (WT3/4),TRUE
513417,"@Override
public void run () {
    final Counter counter = new Counter (""TRANSMIT"", plotter);
    counter.start ();
    try {
        final DataInputStream dis = new DataInputStream (s.getInputStream ());
        while (! Thread.interrupted ()) {
            if (! running.get ()) {
                Thread.sleep (1000);
                continue;
            }
            final int nextPacketSize = dis.readInt ();
            counter.addBytes (INTEGER_BYTES);
            final byte [] packet = new byte [nextPacketSize];
            dis.readFully (packet);
            counter.addBytes (nextPacketSize);
            final long otherSideCrc = dis.readLong ();
            counter.addBytes (CRC_BYTES);
            final CRC32 crc = new CRC32 ();
            crc.update (packet);
            if (otherSideCrc != crc.getValue ()) {
                throw new RuntimeException (""CRC values don't match: this: "" + crc.getValue () + "", other: "" + otherSideCrc);
            }
        }
    } catch (InterruptedException e) {
        System.out.println (""Receiver thread interrupted!"");
    } catch (Exception e) {
        System.err.println (""Unexpected error in receiver thread: "" + e.getMessage ());
    } finally {
        abortLatch.countDown ();
        counter.interrupt ();
    }
}
",6195313,"protected void zipFile (InputStream in, ZipOutputStream zOut, String vPath, long lastModified, File fromArchive, int mode, ZipExtraField [] extra) throws IOException {
    if (entries.contains (vPath)) {
        if (duplicate.equals (""preserve"")) {
            logWhenWriting (vPath + "" already added, skipping"", Project.MSG_INFO);
            return;
        } else if (duplicate.equals (""fail"")) {
            throw new BuildException (""Duplicate file "" + vPath + "" was found and the duplicate "" + ""attribute is 'fail'."");
        } else {
            logWhenWriting (""duplicate file "" + vPath + "" found, adding."", Project.MSG_VERBOSE);
        }

    } else {
        logWhenWriting (""adding entry "" + vPath, Project.MSG_VERBOSE);
    }
    entries.put (vPath, vPath);
    if (! skipWriting) {
        ZipEntry ze = new ZipEntry (vPath);
        ze.setTime (lastModified);
        ze.setMethod (doCompress ? ZipEntry.DEFLATED : ZipEntry.STORED);
        if (! zOut.isSeekable () && ! doCompress) {
            long size = 0;
            CRC32 cal = new CRC32 ();
            if (! in.markSupported ()) {
                ByteArrayOutputStream bos = new ByteArrayOutputStream ();
                byte [] buffer = new byte [BUFFER_SIZE];
                int count = 0;
                do {
                    size += count;
                    cal.update (buffer, 0, count);
                    bos.write (buffer, 0, count);
                    count = in.read (buffer, 0, buffer.length);
                } while (count != - 1);
                in = new ByteArrayInputStream (bos.toByteArray ());
            } else {
                in.mark (Integer.MAX_VALUE);
                byte [] buffer = new byte [BUFFER_SIZE];
                int count = 0;
                do {
                    size += count;
                    cal.update (buffer, 0, count);
                    count = in.read (buffer, 0, buffer.length);
                } while (count != - 1);
                in.reset ();
            }
            ze.setSize (size);
            ze.setCrc (cal.getValue ());
        }
        ze.setUnixMode (mode);
        zOut.putNextEntry (ze);
        if (extra != null) {
            ze.setExtraFields (extra);
        }
        byte [] buffer = new byte [BUFFER_SIZE];
        int count = 0;
        do {
            if (count != 0) {
                zOut.write (buffer, 0, count);
            }
            count = in.read (buffer, 0, buffer.length);
        } while (count != - 1);
    }
    addedFiles.addElement (vPath);
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
3880859,"public static final long crc32 (byte [] data) {
    CRC32 crc32 = new CRC32 ();
    crc32.update (data);
    return crc32.getValue ();
}
",5352578,"protected int writeEntry (ZipOutputStream jar, Filelike entry, ULog log) throws IOException, ValidationException {
    String archiveName = getNameStrategy ().getArchiveName (log, entry);
    if (archiveName != null && archiveName.length () > 0) {
        ZipEntry ze = new ZipEntry (archiveName);
        log.fine (""writing entry {0} ({1} bytes)"", new Quote (ze.getName ()), SIZE_FORMAT.format (entry.getSize ()));
        byte [] bytes = entry.readWhole ();
        if (! compressed) {
            ze.setMethod (ZipEntry.STORED);
            ze.setSize (entry.getSize ());
            ze.setCompressedSize (entry.getSize ());
            CRC32 crc = new CRC32 ();
            crc.update (bytes);
            ze.setCrc (crc.getValue ());
        }
        jar.putNextEntry (ze);
        jar.write (bytes);
        jar.closeEntry ();
        return bytes.length;
    } else {
        return 0;
    }
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
3880859,"public static final long crc32 (byte [] data) {
    CRC32 crc32 = new CRC32 ();
    crc32.update (data);
    return crc32.getValue ();
}
",5277473,"public long computeCRC32 () throws IOException {
    CRC32 compCRC32 = new CRC32 ();
    for (int i = 0;
    i < numDataRecords; i ++) {
        try {
            compCRC32.update (readRecord (i + 1));
        } catch (ArrayIndexOutOfBoundsException e) {
            throw new IOException (""computeCRC32: Index out of bounds reading record "" + (i + 1));
        } catch (IOException e) {
            throw new IOException (""computeCRC32: error reading record "" + (i + 1));
        }
    }
    return compCRC32.getValue ();
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
1874753,"public static Object deleteElements (Object array, int firstElement, int nElements) {
    if (nElements == 0 || array == null) return array;

    int oldLength = Array.getLength (array);
    if (firstElement >= oldLength) return array;

    int n = oldLength - (firstElement + nElements);
    if (n < 0) n = 0;

    Object t = Array.newInstance (array.getClass ().getComponentType (), firstElement + n);
    if (firstElement > 0) System.arraycopy (array, 0, t, 0, firstElement);

    if (n > 0) System.arraycopy (array, firstElement + nElements, t, firstElement, n);

    return t;
}
",11099387,"private static Object extendArray (Object a1) {
    int n = Array.getLength (a1);
    Object a2 = Array.newInstance (a1.getClass ().getComponentType (), n + ARRAY_SIZE_INCREMENT);
    System.arraycopy (a1, 0, a2, 0, n);
    return a2;
}
",Resize Array,Type-3 (WT3/4),TRUE
1347808,"public static void main (String [] args) throws IOException {
    FileOutputStream f = new FileOutputStream (""test.zip"");
    CheckedOutputStream csum = new CheckedOutputStream (f, new Adler32 ());
    ZipOutputStream zos = new ZipOutputStream (csum);
    BufferedOutputStream out = new BufferedOutputStream (zos);
    zos.setComment (""A test of Java Zipping"");
    for (String arg : args) {
        print (""Writing file "" + arg);
        BufferedReader in = new BufferedReader (new FileReader (arg));
        zos.putNextEntry (new ZipEntry (arg));
        int c;
        while ((c = in.read ()) != - 1) out.write (c);

        in.close ();
        out.flush ();
    }
    out.close ();
    print (""Checksum: "" + csum.getChecksum ().getValue ());
    print (""Reading file"");
    FileInputStream fi = new FileInputStream (""test.zip"");
    CheckedInputStream csumi = new CheckedInputStream (fi, new Adler32 ());
    ZipInputStream in2 = new ZipInputStream (csumi);
    BufferedInputStream bis = new BufferedInputStream (in2);
    ZipEntry ze;
    while ((ze = in2.getNextEntry ()) != null) {
        print (""Reading file "" + ze);
        int x;
        while ((x = bis.read ()) != - 1) System.out.write (x);

    }
    if (args.length == 1) print (""Checksum: "" + csumi.getChecksum ().getValue ());

    bis.close ();
    ZipFile zf = new ZipFile (""test.zip"");
    Enumeration e = zf.entries ();
    while (e.hasMoreElements ()) {
        ZipEntry ze2 = (ZipEntry) e.nextElement ();
        print (""File: "" + ze2);
    }
}
",12002709,"private static void zipDirectory (ZipOutputStream zos, File files, String entry) throws IOException {
    if (files.isDirectory ()) {
        if (entry != null) {
            zos.putNextEntry (new ZipEntry (entry + ""/""));
            entry = entry + ""/"";
        } else {
            zos.putNextEntry (new ZipEntry (""/""));
            entry = ""/"";
        }
        String [] names = files.list ();
        File [] files0 = files.listFiles ();
        for (int i = 0;
        i < files0.length; i ++) {
            zipDirectory (zos, files0 [i], entry + names [i]);
        }
        zos.closeEntry ();
    } else {
        if (entry != null) {
            zos.putNextEntry (new ZipEntry (entry));
        }
        byte [] data = new byte [1000];
        BufferedInputStream in = new BufferedInputStream (new FileInputStream (files), 1000);
        int count;
        while ((count = in.read (data, 0, 1000)) != - 1) {
            zos.write (data, 0, count);
        }
        zos.closeEntry ();
        in.close ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
1171511,"public void saveAttributes (Attributes a) throws IOException {
    String extension = fileResourceExtent.getUpperCaseExtension ();
    if (""XML"".equals (extension)) {
        this.saveExtentsXML (a);
    } else {
        File file = new File (fileResourceExtent.getAbsoluteFilename ());
        FileOutputStream fos = new FileOutputStream (file);
        ZipOutputStream zout = new ZipOutputStream (fos);
        zout.putNextEntry (new ZipEntry (""Extents""));
        DataOutputStream out = new DataOutputStream (zout);
        saveExtentsBinary (out, a);
        out.close ();
        fos.close ();
    }
    extension = fileResourceMatrix.getUpperCaseExtension ();
    if (""XML"".equals (extension)) {
    } else {
        File file = new File (fileResourceMatrix.getAbsoluteFilename ());
        FileOutputStream fos = new FileOutputStream (file);
        ZipOutputStream zout = new ZipOutputStream (fos);
        zout.putNextEntry (new ZipEntry (""Matrix""));
        DataOutputStream out = new DataOutputStream (zout);
        saveMatrixBinary (out, a);
        out.close ();
        fos.close ();
    }
    extension = fileResourceAttributes.getUpperCaseExtension ();
    if (""XML"".equals (extension)) {
        this.saveAttributeXML (a);
    } else {
        File file = new File (fileResourceAttributes.getAbsoluteFilename ());
        FileOutputStream fos = new FileOutputStream (file);
        ZipOutputStream zout = new ZipOutputStream (fos);
        zout.putNextEntry (new ZipEntry (""Attributes""));
        DataOutputStream out = new DataOutputStream (zout);
        saveAttributesBinary (out, a);
        out.close ();
        fos.close ();
    }
    String extent_tree_filename_stem = ""extent_tree_"";
    for (int i = 0;
    i < a.getExtents ().size (); i ++) {
        try {
            saveXMLDocument (extent_tree_filename_stem + i + "".xml"", a.getExtents ().at (i).getExtentXML ());
        } catch (Exception e) {
        }
    }
}
",18757376,"public static File zipFile (String pathToBeZipped, String pathZippedFile) throws IOException {
    if (pathZippedFile.indexOf ("".zip"") < 0) {
        pathZippedFile += "".zip"";
    }
    File fileASerZipado = new File (pathToBeZipped);
    byte [] buf = new byte [BUFFER_SIZE];
    ZipOutputStream out = new ZipOutputStream (new FileOutputStream (pathZippedFile));
    FileInputStream in = new FileInputStream (pathToBeZipped);
    out.putNextEntry (new ZipEntry (fileASerZipado.getName ()));
    int len;
    while ((len = in.read (buf)) > 0) {
        out.write (buf, 0, len);
    }
    out.closeEntry ();
    in.close ();
    out.close ();
    return new File (pathZippedFile);
}
",Zip Files,Type-3 (WT3/4),FALSE
1588099,"private void packFile (final File file, final ZipOutputStream out, final String name, final FileFilter filter) throws IOException {
    if (filter != null && ! filter.accept (file)) return;

    if (file.isDirectory ()) {
        final File [] list = file.listFiles ();
        if (list == null) return;

        for (final File element : list) if (name == null) packFile (element, out, file.getName (), filter);
        else packFile (element, out, name + ""/"" + file.getName (), filter);

    } else {
        ZipEntry entry = null;
        if (name == null) entry = new ZipEntry (file.getName ());
        else entry = new ZipEntry (name + ""/"" + file.getName ());

        try {
            out.putNextEntry (entry);
        } catch (final ZipException e) {
            throw new C4JRuntimeException (format (""Could not pack file ‘%s’."", file.getPath ()), e);
        }
        InputStream fileIn = null;
        try {
            fileIn = new FileInputStream (file);
            use_filetools ().copyStream2Stream (fileIn, out);
        } finally {
            if (fileIn != null) fileIn.close ();

        }
        out.closeEntry ();
    }
}
",7320433,"private void writeDynData (int time_s) throws IOException {
    this.zos.putNextEntry (new ZipEntry (""step."" + time_s + "".bin""));
    this.outFile = new DataOutputStream (this.zos);
    this.buf.position (0);
    this.outFile.writeDouble (time_s);
    this.quad.writeDynData (null, this.buf);
    this.outFile.writeInt (this.buf.position ());
    this.outFile.write (this.buf.array (), 0, this.buf.position ());
    this.zos.closeEntry ();
}
",Zip Files,Type-3 (WT3/4),FALSE
16301512,"public static void copy (File src, File dst) throws IOException {
    FileChannel inChannel;
    FileChannel outChannel;
    inChannel = new FileInputStream (src).getChannel ();
    outChannel = new FileOutputStream (dst).getChannel ();
    outChannel.transferFrom (inChannel, 0, inChannel.size ());
    inChannel.close ();
    outChannel.close ();
}
",21246898,"public static void main (String [] args) throws ParseException, FileNotFoundException, IOException {
    InputStream input = new BufferedInputStream (UpdateLanguages.class.getResourceAsStream (""definition_template""));
    Translator t = new Translator (input, ""UTF8"");
    Node template = Translator.Start ();
    File langs = new File (""support/support/translate/languages"");
    for (File f : langs.listFiles ()) {
        if (f.getName ().endsWith ("".lng"")) {
            input = new BufferedInputStream (new FileInputStream (f));
            try {
                Translator.ReInit (input, ""UTF8"");
            } catch (java.lang.NullPointerException e) {
                new Translator (input, ""UTF8"");
            }
            Node newFile = Translator.Start ();
            ArrayList < Addition > additions = new ArrayList < Addition > ();
            syncKeys (template, newFile, additions);
            ArrayList < String > fileLines = new ArrayList < String > ();
            Scanner scanner = new Scanner (new BufferedReader (new FileReader (f)));
            while (scanner.hasNextLine ()) {
                fileLines.add (scanner.nextLine ());
            }
            int offset = 0;
            for (Addition a : additions) {
                System.out.println (""Key added "" + a + "" to "" + f.getName ());
                if (a.afterLine < 0 || a.afterLine >= fileLines.size ()) {
                    fileLines.add (a.getAddition (0));
                } else {
                    fileLines.add (a.afterLine + (offset ++) + 1, a.getAddition (0));
                }
            }
            f.delete ();
            Writer writer = new BufferedWriter (new FileWriter (f));
            for (String s : fileLines) writer.write (s + ""\n"");

            writer.close ();
            System.out.println (""Language "" + f.getName () + "" had "" + additions.size () + "" additions"");
        }
    }
    File defFile = new File (langs, ""language.lng"");
    defFile.delete ();
    defFile.createNewFile ();
    InputStream copyStream = new BufferedInputStream (UpdateLanguages.class.getResourceAsStream (""definition_template""));
    OutputStream out = new BufferedOutputStream (new FileOutputStream (defFile));
    int c = 0;
    while ((c = copyStream.read ()) >= 0) out.write (c);

    out.close ();
    System.out.println (""Languages updated."");
}
",Copy File,Type-3 (WT3/4),TRUE
12440169,"public String openFileAsText (String resource) throws IOException {
    StringWriter wtr = new StringWriter ();
    InputStreamReader rdr = new InputStreamReader (openFile (resource));
    try {
        IOUtils.copy (rdr, wtr);
    } finally {
        IOUtils.closeQuietly (rdr);
    }
    return wtr.toString ();
}
",17456566,"public static boolean decodeFileToFile (String infile, String outfile) {
    boolean success = false;
    java.io.InputStream in = null;
    java.io.OutputStream out = null;
    try {
        in = new Base64.InputStream (new java.io.BufferedInputStream (new java.io.FileInputStream (infile)), Base64.DECODE);
        out = new java.io.BufferedOutputStream (new java.io.FileOutputStream (outfile));
        byte [] buffer = new byte [65536];
        int read = - 1;
        while ((read = in.read (buffer)) >= 0) {
            out.write (buffer, 0, read);
        }
        success = true;
    } catch (java.io.IOException exc) {
        exc.printStackTrace ();
    } finally {
        try {
            in.close ();
        } catch (Exception exc) {
        }
        try {
            out.close ();
        } catch (Exception exc) {
        }
    }
    return success;
}
",Copy File,Type-3 (WT3/4),TRUE
6008880,"protected void updateJava2ScriptProject (String prjFolder, String binRelative) {
    try {
        File cpFile = new File (prjFolder, "".classpath"");
        FileInputStream fis = new FileInputStream (cpFile);
        String classpath = J2SLaunchingUtil.readAFile (fis);
        if (classpath != null) {
            boolean needUpdate = false;
            if (classpath.indexOf (""ECLIPSE_SWT"") == - 1 && classpath.indexOf (""SWT_LIBRARY"") == - 1 && classpath.indexOf (""eclipse.swt"") == - 1) {
                int idx = classpath.lastIndexOf (""<"");
                classpath = classpath.substring (0, idx) + ""\t<classpathentry kind=\""var\"" path=\""ECLIPSE_SWT\""/>\r\n"" + classpath.substring (idx);
                needUpdate = true;
            }
            if (classpath.indexOf (""AJAX_SWT"") == - 1 && classpath.indexOf (""ajaxswt.jar"") == - 1) {
                int idx = classpath.lastIndexOf (""<"");
                classpath = classpath.substring (0, idx) + ""\t<classpathentry sourcepath=\""AJAX_SWT_SRC\"" kind=\""var\"" path=\""AJAX_SWT\""/>\r\n"" + classpath.substring (idx);
                needUpdate = true;
            }
            if (classpath.indexOf (""AJAX_RPC"") == - 1 && classpath.indexOf (""ajaxrpc.jar"") == - 1) {
                int idx = classpath.lastIndexOf (""<"");
                classpath = classpath.substring (0, idx) + ""\t<classpathentry sourcepath=\""AJAX_RPC_SRC\"" kind=\""var\"" path=\""AJAX_RPC\""/>\r\n"" + classpath.substring (idx);
                needUpdate = true;
            }
            if (classpath.indexOf (""AJAX_PIPE"") == - 1 && classpath.indexOf (""ajaxpipe.jar"") == - 1) {
                int idx = classpath.lastIndexOf (""<"");
                classpath = classpath.substring (0, idx) + ""\t<classpathentry sourcepath=\""AJAX_PIPE_SRC\"" kind=\""var\"" path=\""AJAX_PIPE\""/>\r\n"" + classpath.substring (idx);
                needUpdate = true;
            }
            if (needUpdate) {
                try {
                    FileOutputStream fos = new FileOutputStream (cpFile);
                    fos.write (classpath.getBytes (""utf-8""));
                    fos.close ();
                } catch (FileNotFoundException e) {
                    e.printStackTrace ();
                } catch (IOException e) {
                    e.printStackTrace ();
                }
            }
        }
        File webinf = new File (prjFolder, ""WEB-INF"");
        webinf.mkdir ();
        new File (webinf, ""classes"").mkdir ();
        File lib = new File (webinf, ""lib"");
        lib.mkdir ();
        IPath newPath = null;
        URL starterURL = AjaxPlugin.getDefault ().getBundle ().getEntry (File.separator);
        String root = ""."";
        try {
            root = Platform.asLocalURL (starterURL).getFile ();
        } catch (IOException e1) {
            e1.printStackTrace ();
        }
        newPath = Path.fromPortableString (root + ""/ajaxrpc.jar"");
        File rpcFile = new File (newPath.toOSString ());
        try {
            FileInputStream is = new FileInputStream (rpcFile);
            FileOutputStream os = new FileOutputStream (new File (lib, ""ajaxrpc.jar""));
            byte [] buf = new byte [1024];
            int read = - 1;
            while ((read = is.read (buf)) != - 1) {
                os.write (buf, 0, read);
            }
            os.close ();
            is.close ();
        } catch (IOException e1) {
            e1.printStackTrace ();
        }
        newPath = Path.fromPortableString (root + ""/ajaxpipe.jar"");
        File pipeFile = new File (newPath.toOSString ());
        try {
            FileInputStream is = new FileInputStream (pipeFile);
            FileOutputStream os = new FileOutputStream (new File (lib, ""ajaxpipe.jar""));
            byte [] buf = new byte [1024];
            int read = - 1;
            while ((read = is.read (buf)) != - 1) {
                os.write (buf, 0, read);
            }
            os.close ();
            is.close ();
        } catch (IOException e1) {
            e1.printStackTrace ();
        }
        StringBuffer buildxml = new StringBuffer ();
        buildxml.append (""<?xml version=\""1.0\""?>\r\n"");
        buildxml.append (""<project name=\""java2script.servlet.pack\"" default=\""pack.war\"" basedir=\"".\"">\r\n"");
        buildxml.append (""    <description>Pack Java2Script Servlet Application</description>\r\n"");
        buildxml.append (""\r\n"");
        String name = new File (prjFolder).getName ();
        buildxml.append (""	<property name=\""java2script.app.name\"" value=\"""" + name + ""\""/>\r\n"");
        buildxml.append (""	<property name=\""bin.folder\"" value=\""${basedir}/../"" + binRelative + ""\""/>\r\n"");
        buildxml.append (""\r\n"");
        buildxml.append (""    <target name=\""pack.war\"" depends=\""pack.jar\"">\r\n"");
        buildxml.append (""        <tstamp>\r\n"");
        buildxml.append (""            <format property=\""now\"" pattern=\""yyyy-MM-dd-HH-mm-ss\""/>\r\n"");
        buildxml.append (""        </tstamp>\r\n"");
        buildxml.append (""        <delete file=\""${basedir}/../${java2script.app.name}.war\"" quiet=\""true\""/>\r\n"");
        buildxml.append (""        <zip destfile=\""${basedir}/../${java2script.app.name}.${now}.war\"">\r\n"");
        buildxml.append (""            <fileset dir=\""${basedir}/../\"">\r\n"");
        buildxml.append (""                <exclude name=\""src/**\""/>\r\n"");
        buildxml.append (""                <exclude name=\""META-INF/**\""/>\r\n"");
        buildxml.append (""                <exclude name=\""WEB-INF/**\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.java\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.class\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.swp\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.swo\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.jar\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.war\""/>\r\n"");
        buildxml.append (""                <exclude name=\"".classpath\""/>\r\n"");
        buildxml.append (""                <exclude name=\"".project\""/>\r\n"");
        buildxml.append (""                <exclude name=\"".j2s\""/>\r\n"");
        buildxml.append (""                <exclude name=\""web.xml\""/>\r\n"");
        buildxml.append (""                <exclude name=\""build.xml\""/>\r\n"");
        buildxml.append (""                <exclude name=\""build.properties\""/>\r\n"");
        buildxml.append (""                <exclude name=\""plugin.xml\""/>\r\n"");
        buildxml.append (""                <exclude name=\""plugin.properties\""/>\r\n"");
        buildxml.append (""            </fileset>\r\n"");
        buildxml.append (""            <fileset dir=\""${basedir}/..\"">\r\n"");
        buildxml.append (""                <include name=\""WEB-INF/**\""/>\r\n"");
        buildxml.append (""                <exclude name=\""WEB-INF/build.xml\""/>\r\n"");
        buildxml.append (""            </fileset>\r\n"");
        buildxml.append (""        </zip>\r\n"");
        buildxml.append (""        <copy file=\""${basedir}/../${java2script.app.name}.${now}.war\""\r\n"");
        buildxml.append (""                tofile=\""${basedir}/../${java2script.app.name}.war\""/>\r\n"");
        buildxml.append (""    </target>\r\n"");
        buildxml.append (""\r\n"");
        buildxml.append (""    <target name=\""pack.jar\"">\r\n"");
        buildxml.append (""        <delete file=\""${basedir}/lib/${java2script.app.name}.jar\"" quiet=\""true\""/>\r\n"");
        buildxml.append (""        <zip destfile=\""${basedir}/lib/${java2script.app.name}.jar\"">\r\n"");
        buildxml.append (""            <fileset dir=\""${bin.folder}\"">\r\n"");
        buildxml.append (""                <exclude name=\""WEB-INF/**\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.html\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.js\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.css\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.bmp\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.gif\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.png\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.jpg\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.jpeg\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.swp\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.swo\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.jar\""/>\r\n"");
        buildxml.append (""                <exclude name=\""**/*.war\""/>\r\n"");
        buildxml.append (""                <exclude name=\"".classpath\""/>\r\n"");
        buildxml.append (""                <exclude name=\"".project\""/>\r\n"");
        buildxml.append (""                <exclude name=\"".j2s\""/>\r\n"");
        buildxml.append (""                <exclude name=\""web.xml\""/>\r\n"");
        buildxml.append (""                <exclude name=\""build.xml\""/>\r\n"");
        buildxml.append (""                <exclude name=\""build.properties\""/>\r\n"");
        buildxml.append (""                <exclude name=\""plugin.xml\""/>\r\n"");
        buildxml.append (""                <exclude name=\""plugin.properties\""/>\r\n"");
        buildxml.append (""            </fileset>\r\n"");
        buildxml.append (""        </zip>\r\n"");
        buildxml.append (""    </target>\r\n"");
        buildxml.append (""\r\n"");
        starterURL = AjaxPlugin.getDefault ().getBundle ().getEntry (File.separator);
        root = ""."";
        try {
            root = Platform.asLocalURL (starterURL).getFile ();
        } catch (IOException e1) {
            e1.printStackTrace ();
        }
        newPath = Path.fromPortableString (root);
        String ajaxPath = newPath.toOSString ();
        String key = ""net.sf.j2s.ajax"";
        int idx = ajaxPath.lastIndexOf (key);
        if (idx != - 1) {
            ajaxPath = ajaxPath.substring (0, idx) + ""net.sf.j2s.lib"" + ajaxPath.substring (idx + key.length ());
        }
        File libFile = new File (ajaxPath);
        String j2sRelativePath = FileUtil.toRelativePath (libFile.getAbsolutePath (), webinf.getAbsolutePath ());
        if (j2sRelativePath.length () > 0 && ! j2sRelativePath.endsWith (""/"")) {
            j2sRelativePath += ""/"";
        }
        int slashIndex = j2sRelativePath.lastIndexOf ('/', j2sRelativePath.length () - 2);
        String pluginPath = j2sRelativePath.substring (0, slashIndex);
        String libPluginPath = j2sRelativePath.substring (slashIndex + 1, j2sRelativePath.length () - 1);
        buildxml.append (""    <target name=\""pack.plugins.j2slib.war\"">\r\n"");
        buildxml.append (""        <delete file=\""${basedir}/../plugins.war\"" quiet=\""true\""/>\r\n"");
        buildxml.append (""        <zip destfile=\""${basedir}/../plugins.war\"">\r\n"");
        buildxml.append (""            <fileset dir=\""${basedir}/"" + pluginPath + ""/\"">\r\n"");
        buildxml.append (""                <include name=\"""" + libPluginPath + ""/**\""/>\r\n"");
        buildxml.append (""                <exclude name=\"""" + libPluginPath + ""/library.jar\""/>\r\n"");
        buildxml.append (""                <exclude name=\"""" + libPluginPath + ""/plugin.xml\""/>\r\n"");
        buildxml.append (""                <exclude name=\"""" + libPluginPath + ""/META-INF/**\""/>\r\n"");
        buildxml.append (""            </fileset>\r\n"");
        buildxml.append (""        </zip>\r\n"");
        buildxml.append (""    </target>\r\n"");
        buildxml.append (""\r\n"");
        buildxml.append (""</project>\r\n"");
        try {
            FileOutputStream fos = new FileOutputStream (new File (webinf, ""build.xml""));
            fos.write (buildxml.toString ().getBytes ());
            fos.close ();
        } catch (FileNotFoundException e) {
            e.printStackTrace ();
        } catch (IOException e) {
            e.printStackTrace ();
        }
        StringBuffer webxml = new StringBuffer ();
        webxml.append (""<?xml version=\""1.0\"" encoding=\""ISO-8859-1\""?>\r\n"");
        webxml.append (""<!DOCTYPE web-app\r\n"");
        webxml.append (""    PUBLIC \""-//Sun Microsystems, Inc.//DTD Web Application 2.3//EN\""\r\n"");
        webxml.append (""    \""http://java.sun.com/dtd/web-app_2_3.dtd\"">\r\n"");
        webxml.append (""<web-app>\r\n"");
        webxml.append (""    <display-name>Java2Script</display-name>\r\n"");
        webxml.append (""    <description>Java2Script application</description>\r\n"");
        webxml.append (genereateServlet (""simplerpc"", ""net.sf.j2s.ajax.SimpleRPCHttpServlet""));
        webxml.append (genereateServlet (""piperpc"", ""net.sf.j2s.ajax.CompoundPipeRPCHttpServlet""));
        webxml.append (""    <servlet>\r\n"");
        webxml.append (""        <servlet-name>simplepipe</servlet-name>\r\n"");
        webxml.append (""        <servlet-class>net.sf.j2s.ajax.SimplePipeHttpServlet</servlet-class>\r\n"");
        webxml.append (""        <init-param>\r\n"");
        webxml.append (""            <param-name>simple.pipe.query.timeout</param-name>\r\n"");
        webxml.append (""            <param-value>20000</param-value>\r\n"");
        webxml.append (""        </init-param>\r\n"");
        webxml.append (""        <init-param>\r\n"");
        webxml.append (""            <param-name>simple.pipe.script.breakout</param-name>\r\n"");
        webxml.append (""            <param-value>1200000</param-value>\r\n"");
        webxml.append (""        </init-param>\r\n"");
        webxml.append (""        <init-param>\r\n"");
        webxml.append (""            <param-name>simple.pipe.max.items.per.query</param-name>\r\n"");
        webxml.append (""            <param-value>60</param-value>\r\n"");
        webxml.append (""        </init-param>\r\n"");
        webxml.append (""    </servlet>\r\n"");
        webxml.append (""    <servlet-mapping>\r\n"");
        webxml.append (""        <servlet-name>simplerpc</servlet-name>\r\n"");
        webxml.append (""        <url-pattern>/simplerpc</url-pattern>\r\n"");
        webxml.append (""    </servlet-mapping>\r\n"");
        webxml.append (""    <servlet-mapping>\r\n"");
        webxml.append (""        <servlet-name>piperpc</servlet-name>\r\n"");
        webxml.append (""        <url-pattern>/piperpc</url-pattern>\r\n"");
        webxml.append (""    </servlet-mapping>\r\n"");
        webxml.append (""    <servlet-mapping>\r\n"");
        webxml.append (""        <servlet-name>simplepipe</servlet-name>\r\n"");
        webxml.append (""        <url-pattern>/simplepipe</url-pattern>\r\n"");
        webxml.append (""    </servlet-mapping>\r\n"");
        webxml.append (""</web-app>\r\n"");
        try {
            FileOutputStream fos = new FileOutputStream (new File (webinf, ""web.xml""));
            fos.write (webxml.toString ().getBytes ());
            fos.close ();
        } catch (FileNotFoundException e) {
            e.printStackTrace ();
        } catch (IOException e) {
            e.printStackTrace ();
        }
    } catch (FileNotFoundException e1) {
        e1.printStackTrace ();
    }
}
",21057438,"public void run () {
    try {
        Socket socket = getSocket ();
        System.out.println (""opening socket to "" + address + "" on "" + port);
        InputStream in = socket.getInputStream ();
        for (;;) {
            FileTransferHeader header = FileTransferHeader.readHeader (in);
            if (header == null) break;

            System.out.println (""header: "" + header);
            String [] parts = header.getFilename ().getSegments ();
            String filename;
            if (parts.length > 0) filename = ""dl-"" + parts [parts.length - 1];
            else filename = ""dl-"" + session.getScreenname ();

            System.out.println (""writing to file "" + filename);
            long sum = 0;
            if (new File (filename).exists ()) {
                FileInputStream fis = new FileInputStream (filename);
                byte [] block = new byte [10];
                for (int i = 0;
                i < block.length;) {
                    int count = fis.read (block);
                    if (count == - 1) break;

                    i += count;
                }
                FileTransferChecksum summer = new FileTransferChecksum ();
                summer.update (block, 0, 10);
                sum = summer.getValue ();
            }
            FileChannel fileChannel = new FileOutputStream (filename).getChannel ();
            FileTransferHeader outHeader = new FileTransferHeader (header);
            outHeader.setHeaderType (FileTransferHeader.HEADERTYPE_ACK);
            outHeader.setIcbmMessageId (cookie);
            outHeader.setBytesReceived (0);
            outHeader.setReceivedChecksum (sum);
            OutputStream socketOut = socket.getOutputStream ();
            System.out.println (""sending header: "" + outHeader);
            outHeader.write (socketOut);
            for (int i = 0;
            i < header.getFileSize ();) {
                long transferred = fileChannel.transferFrom (Channels.newChannel (in), 0, header.getFileSize () - i);
                System.out.println (""transferred "" + transferred);
                if (transferred == - 1) return;

                i += transferred;
            }
            System.out.println (""finished transfer!"");
            fileChannel.close ();
            FileTransferHeader doneHeader = new FileTransferHeader (header);
            doneHeader.setHeaderType (FileTransferHeader.HEADERTYPE_RECEIVED);
            doneHeader.setFlags (doneHeader.getFlags () | FileTransferHeader.FLAG_DONE);
            doneHeader.setBytesReceived (doneHeader.getBytesReceived () + 1);
            doneHeader.setIcbmMessageId (cookie);
            doneHeader.setFilesLeft (doneHeader.getFilesLeft () - 1);
            doneHeader.write (socketOut);
            if (doneHeader.getFilesLeft () - 1 <= 0) {
                socket.close ();
                break;
            }
        }
    } catch (IOException e) {
        e.printStackTrace ();
        return;
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1093295,"private static void createZip (final File destinationFile, final List < File > files, final int cutFileNameIndex) throws IOException {
    final ZipOutputStream oStream = new ZipOutputStream (new FileOutputStream (destinationFile));
    for (final File file : files) {
        final String fullFileName = file.getAbsolutePath ();
        final String cuttedFileName = fullFileName.substring (cutFileNameIndex);
        final String osIndependendFileName = cuttedFileName.replace (File.separatorChar, '/');
        oStream.putNextEntry (new ZipEntry (osIndependendFileName));
        final FileInputStream iStream = new FileInputStream (file);
        FileOperations.copy (iStream, oStream);
        oStream.closeEntry ();
        iStream.close ();
    }
    oStream.close ();
}
",6195313,"protected void zipFile (InputStream in, ZipOutputStream zOut, String vPath, long lastModified, File fromArchive, int mode, ZipExtraField [] extra) throws IOException {
    if (entries.contains (vPath)) {
        if (duplicate.equals (""preserve"")) {
            logWhenWriting (vPath + "" already added, skipping"", Project.MSG_INFO);
            return;
        } else if (duplicate.equals (""fail"")) {
            throw new BuildException (""Duplicate file "" + vPath + "" was found and the duplicate "" + ""attribute is 'fail'."");
        } else {
            logWhenWriting (""duplicate file "" + vPath + "" found, adding."", Project.MSG_VERBOSE);
        }

    } else {
        logWhenWriting (""adding entry "" + vPath, Project.MSG_VERBOSE);
    }
    entries.put (vPath, vPath);
    if (! skipWriting) {
        ZipEntry ze = new ZipEntry (vPath);
        ze.setTime (lastModified);
        ze.setMethod (doCompress ? ZipEntry.DEFLATED : ZipEntry.STORED);
        if (! zOut.isSeekable () && ! doCompress) {
            long size = 0;
            CRC32 cal = new CRC32 ();
            if (! in.markSupported ()) {
                ByteArrayOutputStream bos = new ByteArrayOutputStream ();
                byte [] buffer = new byte [BUFFER_SIZE];
                int count = 0;
                do {
                    size += count;
                    cal.update (buffer, 0, count);
                    bos.write (buffer, 0, count);
                    count = in.read (buffer, 0, buffer.length);
                } while (count != - 1);
                in = new ByteArrayInputStream (bos.toByteArray ());
            } else {
                in.mark (Integer.MAX_VALUE);
                byte [] buffer = new byte [BUFFER_SIZE];
                int count = 0;
                do {
                    size += count;
                    cal.update (buffer, 0, count);
                    count = in.read (buffer, 0, buffer.length);
                } while (count != - 1);
                in.reset ();
            }
            ze.setSize (size);
            ze.setCrc (cal.getValue ());
        }
        ze.setUnixMode (mode);
        zOut.putNextEntry (ze);
        if (extra != null) {
            ze.setExtraFields (extra);
        }
        byte [] buffer = new byte [BUFFER_SIZE];
        int count = 0;
        do {
            if (count != 0) {
                zOut.write (buffer, 0, count);
            }
            count = in.read (buffer, 0, buffer.length);
        } while (count != - 1);
    }
    addedFiles.addElement (vPath);
}
",Zip Files,Type-3 (WT3/4),FALSE
4736223,"public int checksum () {
    if (checksumset) return checksum_value;

    CRC32 crc32 = new CRC32 ();
    crc32.update ((byte) channel);
    crc32.update ((byte) program);
    crc32.update ((byte) pitchbend_data1);
    crc32.update ((byte) pitchbend_data2);
    for (int i = 0;
    i < events.length; i ++) {
        crc32.update (events [i].getMessage ().getMessage ());
    }
    if (controls != null) {
        int [] sorted = new int [controls.length];
        for (int i = 0;
        i < controls.length; i ++) {
            sorted [i] = (controls [i] << 2) + controls_values [i];
        }
        Arrays.sort (sorted);
        for (int i = 0;
        i < sorted.length; i ++) {
            crc32.update ((byte) (sorted [i] & 0xFF));
            crc32.update ((byte) ((sorted [i] & 0xFF00)>> 2));
        }
    }
    if (activenotes != null) {
        int [] sorted = new int [activenotes.length];
        for (int i = 0;
        i < activenotes.length; i ++) {
            sorted [i] = (activenotes [i] << 2) + activenotes_velocity [i];
        }
        Arrays.sort (sorted);
        for (int i = 0;
        i < sorted.length; i ++) {
            crc32.update ((byte) (sorted [i] & 0xFF));
            crc32.update ((byte) ((sorted [i] & 0xFF00)>> 2));
        }
    }
    checksumset = true;
    checksum_value = (int) crc32.getValue ();
    return checksum_value;
}
",20943990,"private long getCRC (InputStream stream) {
    CRC32 crc = new CRC32 ();
    try {
        byte [] buffer = new byte [1024];
        int length;
        while ((length = stream.read (buffer)) != - 1) {
            crc.update (buffer, 0, length);
        }
    } catch (IOException e) {
        IdeLog.logError (SyncingPlugin.getDefault (), ""Error retrieving CRC"", e);
    }
    return crc.getValue ();
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
3456233,"public ActionForward downloadDS (ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception {
    if (log.isDebugEnabled ()) {
        log.debug (""Entering 'datastore download' method"");
    }
    DocServiceManager mgr = (DocServiceManager) getBean (""docServiceManager"");
    List < Document > docsInDS = mgr.listDocuments ();
    response.setContentType (""application/zip"");
    response.setHeader (""Content-Disposition"", ""attachment; filename=\"""" + ""safe-ds.zip\"""");
    ZipOutputStream zipOut = new ZipOutputStream (response.getOutputStream ());
    try {
        CRC32 crc = new CRC32 ();
        for (Document doc : docsInDS) {
            String fileName = doc.getDocumentID ();
            if (! fileName.endsWith ("".xml"")) {
                fileName += "".xml"";
            }
            byte [] docData = mgr.getDocXML (doc.getDocumentID ());
            ZipEntry entry = new ZipEntry (fileName);
            entry.setSize (docData.length);
            crc.reset ();
            crc.update (docData);
            entry.setCrc (crc.getValue ());
            zipOut.putNextEntry (entry);
            try {
                zipOut.write (docData);
            } finally {
                zipOut.closeEntry ();
            }
        }
    } finally {
        zipOut.close ();
    }
    return null;
}
",8347589,"protected void commonInit (String displayName, IDataSource [] dataSource, Unit unit) {
    this.displayName = displayName;
    CRC32 crc = new CRC32 ();
    crc.update (canonicalName.getBytes ());
    this.hashedId = crc.getValue ();
    this.unit = unit;
    this.cursors = new long [this.dataSources.length];
    getStreamManager ().addStream (this);
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
1086128,"public void streamDataToZip (VolumeTimeSeries vol, ZipOutputStream zout) throws Exception {
    ZipEntry entry = new ZipEntry (vol.getId () + "".dat"");
    zout.putNextEntry (entry);
    if (vol instanceof FloatVolumeTimeSeries) {
        streamData (((FloatVolumeTimeSeries) vol).getData (), zout);
    } else if (vol instanceof RGBVolumeTimeSeries) {
        streamData (((RGBVolumeTimeSeries) vol).getARGBData (), zout);
    } else if (vol instanceof BinaryVolumeTimeSeries) {
        streamData (((BinaryVolumeTimeSeries) vol).getBinaryData (), zout);
    }

}
",8504294,"private void storeProcessList (Date date, List < ProcessList > processListes, boolean doNotOverrideFile) {
    final int BUFFER = 2048;
    String filename = BASE_FILES_PATH + serverGroup + ""/processlist/"" + sdf.format (date) + "".zip"";
    if (doNotOverrideFile && new File (filename).exists ()) return;

    try {
        FileOutputStream dest = new FileOutputStream (filename);
        ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest));
        byte data [] = new byte [BUFFER];
        for (ProcessList processList : processListes) {
            ByteArrayInputStream fi = new ByteArrayInputStream (buildProcessListText (processList).getBytes ());
            BufferedInputStream origin = new BufferedInputStream (fi, BUFFER);
            ZipEntry entry = new ZipEntry (processList.getMysqlServer ().getName () + "".txt"");
            out.putNextEntry (entry);
            int count;
            while ((count = origin.read (data, 0, BUFFER)) != - 1) {
                out.write (data, 0, count);
            }
            origin.close ();
        }
        out.close ();
    } catch (Exception e) {
        e.printStackTrace ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
621362,"private static void readAndRewrite (File inFile, File outFile) throws IOException {
    ImageInputStream iis = ImageIO.createImageInputStream (new BufferedInputStream (new FileInputStream (inFile)));
    DcmParser dcmParser = DcmParserFactory.getInstance ().newDcmParser (iis);
    Dataset ds = DcmObjectFactory.getInstance ().newDataset ();
    dcmParser.setDcmHandler (ds.getDcmHandler ());
    dcmParser.parseDcmFile (null, Tags.PixelData);
    PixelDataReader pdReader = pdFact.newReader (ds, iis, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    System.out.println (""reading "" + inFile + ""..."");
    pdReader.readPixelData (false);
    ImageOutputStream out = ImageIO.createImageOutputStream (new BufferedOutputStream (new FileOutputStream (outFile)));
    DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE;
    ds.writeDataset (out, dcmEncParam);
    ds.writeHeader (out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR (), dcmParser.getReadLength ());
    System.out.println (""writing "" + outFile + ""..."");
    PixelDataWriter pdWriter = pdFact.newWriter (pdReader.getPixelDataArray (), false, ds, out, dcmParser.getDcmDecodeParam ().byteOrder, dcmParser.getReadVR ());
    pdWriter.writePixelData ();
    out.flush ();
    out.close ();
    System.out.println (""done!"");
}
",18809148,"public static void moveOutputAsmFile (File inputLocation, File outputLocation) throws Exception {
    FileInputStream inputStream = null;
    FileOutputStream outputStream = null;
    try {
        inputStream = new FileInputStream (inputLocation);
        outputStream = new FileOutputStream (outputLocation);
        byte buffer [] = new byte [1024];
        while (inputStream.available () > 0) {
            int read = inputStream.read (buffer);
            outputStream.write (buffer, 0, read);
        }
        inputLocation.delete ();
    } finally {
        IOUtil.closeAndIgnoreErrors (inputStream);
        IOUtil.closeAndIgnoreErrors (outputStream);
    }
}
",Copy File,Type-3 (WT3/4),TRUE
15570948,"private String generate (String value) throws Exception {
    String resStr = null;
    try {
        MessageDigest md = MessageDigest.getInstance (""MD5"");
        md.update (value.getBytes (""utf-8""), 0, value.length ());
        byte [] result = md.digest ();
        resStr = FTGenerate.convertToHex (result);
        md.reset ();
    } catch (NoSuchAlgorithmException nae) {
        this.getLog ().severe (""Hash no funcionando"");
        nae.printStackTrace ();
        throw new Exception (""Hash no funcionando"");
    } catch (UnsupportedEncodingException ee) {
        this.getLog ().severe (""Encoding no funcionando"");
        ee.printStackTrace ();
        throw new Exception (""Encoding no funcionando"");
    }
    return resStr;
}
",23034378,"private JeeObserverServerContext (JeeObserverServerContextProperties properties) throws DatabaseException, ServerException {
    super ();
    try {
        final MessageDigest md5 = MessageDigest.getInstance (""MD5"");
        md5.update ((""JE"" + System.currentTimeMillis ()).getBytes ());
        final BigInteger hash = new BigInteger (1, md5.digest ());
        this.sessionId = hash.toString (16).toUpperCase ();
    } catch (final Exception e) {
        this.sessionId = ""JE"" + System.currentTimeMillis ();
        JeeObserverServerContext.logger.log (Level.WARNING, ""JeeObserver Server session ID MD5 error: {0}"", this.sessionId);
        JeeObserverServerContext.logger.log (Level.FINEST, e.getMessage (), e);
    }
    try {
        @SuppressWarnings(""unchecked"")
        final Class < DatabaseHandler > databaseHandlerClass = (Class < DatabaseHandler >) Class.forName (properties.getDatabaseHandler ());
        final Constructor < DatabaseHandler > handlerConstructor = databaseHandlerClass.getConstructor (new Class < ? > [] {String.class, String.class, String.class, String.class, String.class, Integer.class});
        this.databaseHandler = handlerConstructor.newInstance (new Object [] {properties.getDatabaseDriver (), properties.getDatabaseUrl (), properties.getDatabaseUser (), properties.getDatabasePassword (), properties.getDatabaseSchema (), new Integer (properties.getDatabaseConnectionPoolSize ())});
    } catch (final Exception e) {
        throw new ServerException (""Database handler loading exception."", e);
    }
    this.databaseHandlerTimer = new Timer (JeeObserverServerContext.DATABASE_HANDLER_TASK_NAME, true);
    this.server = new JeeObserverServer (properties.getServerPort ());
    this.enabled = true;
    this.properties = properties;
    this.startTimestamp = new Date ();
    try {
        this.ip = InetAddress.getLocalHost ().getHostAddress ();
    } catch (final UnknownHostException e) {
        JeeObserverServerContext.logger.log (Level.SEVERE, e.getMessage (), e);
    }
    this.operatingSystemName = System.getProperty (""os.name"");
    this.operatingSystemVersion = System.getProperty (""os.version"");
    this.operatingSystemArchitecture = System.getProperty (""os.arch"");
    this.javaVersion = System.getProperty (""java.version"");
    this.javaVendor = System.getProperty (""java.vendor"");
}
",Secure Hash,Type-3 (WT3/4),TRUE
2767060,"void process (SourceMetricsDataBuilder data) {
    data.set (SourceMetricsData.SIZE, size);
    Set < String > operators = new HashSet < String > ();
    int standAlone = 0;
    for (SourceTokens.Token token : sourceTokens) {
        if (token.isEOF ()) {
            SourceTokens.Token prev = token.previousToken ();
            if (null == prev) {
                data.set (SourceMetricsData.LINES, 0);
            } else if (prev.getTokenText ().endsWith (""\r"") || prev.getTokenText ().endsWith (""\n"")) {
                data.set (SourceMetricsData.LINES, token.getLineNumber () - 1L);
            } else {
                data.set (SourceMetricsData.LINES, token.getLineNumber ());
            }

            break;
        }
        if (token.isLineComment ()) {
            if (isFirstOnLine (token)) {
                data.bump (SourceMetricsData.LINE_COMMENT);
                if (endOfMultipleLineComments (token)) {
                    bumpCommentLocationMetrics (data, token);
                }
            }
        } else if (token.isBlockComment ()) {
            processMultilineComment (data, token, SourceMetricsData.BLOCK_COMMENT);
        } else if (token.isJavadocComment ()) {
            processMultilineComment (data, token, SourceMetricsData.DOC_COMMENT);
        } else if (token.isWhitespace ()) {
            int lineCount = token.getNewlineCount ();
            SourceTokens.Token prev = token.previousToken ();
            if ((null != prev) && prev.isLineComment ()) {
                lineCount ++;
            }
            if (1 < lineCount) {
                data.bump (SourceMetricsData.WHITESPACE, lineCount - 1L);
            }
        } else if ("";"".equals (token.getTokenText ())) {
            data.bump (SourceMetricsData.LOGICAL_LINES);
        } else if (- 1 != ""(){}"".indexOf (token.getTokenText ())) {
            if (isAloneOnLine (token)) {
                standAlone ++;
            }
        }

        if (token.isLiteral ()) {
            data.bump (SourceMetricsData.OPERANDS);
        } else if (! token.isComment () && ! token.isWhitespace ()) {
            data.bump (SourceMetricsData.OPERATORS);
            operators.add (token.getTokenText ());
        }

    }
    data.set (SourceMetricsData.UNIQUE_OPERATORS, operators.size ());
    data.set (SourceMetricsData.LOC, data.get (SourceMetricsData.LINES) - data.get (SourceMetricsData.WHITESPACE) - data.get (SourceMetricsData.LINE_COMMENT) - data.get (SourceMetricsData.BLOCK_COMMENT) - data.get (SourceMetricsData.DOC_COMMENT));
    data.set (SourceMetricsData.ELOC, data.get (SourceMetricsData.LOC) - standAlone);
    data.set (SourceMetricsData.COMMENTS, data.get (SourceMetricsData.LINE_COMMENT) + data.get (SourceMetricsData.BLOCK_COMMENT) + data.get (SourceMetricsData.DOC_COMMENT));
    String chunk = new String (sourceTokens.getChunk ());
    byte [] bytes = chunk.getBytes ();
    CRC32 crc = new CRC32 ();
    crc.update (bytes);
    data.set (SourceMetricsData.CRC, Double.longBitsToDouble (crc.getValue ()));
}
",12611963,"public static String generateEmailHash (String email) {
    email = email.trim ().toLowerCase ();
    CRC32 crc = new CRC32 ();
    crc.update (email.getBytes ());
    String md5 = generateMD5 (email);
    return crc.getValue () + ""_"" + md5;
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
225907,"private int CalculateTreeWidth (int myGraph [] [], int SolutionVector [], int zaehler) {
    int [] [] TreeDecompositionGraph;
    int [] [] DecompositionedMatrix;
    int [] ConnectedNodes;
    int [] NextSolutionVector;
    int TreeWidth;
    int NumVerticesOfMyGraph;
    int DeeperTreeWidth;
    int LineIndex;
    NumVerticesOfMyGraph = myGraph.length;
    DecompositionedMatrix = new int [NumVerticesOfMyGraph - 1] [NumVerticesOfMyGraph - 1];
    ConnectedNodes = new int [NumVerticesOfMyGraph];
    TreeWidth = 0;
    DeeperTreeWidth = 0;
    LineIndex = 0;
    NextSolutionVector = new int [SolutionVector.length - 1];
    for (int i = 1;
    i < NumVerticesOfMyGraph; i ++) {
        if (SolutionVector [0] == myGraph [i] [0]) {
            LineIndex = i;
        }
    }
    for (int j = 1;
    j < NumVerticesOfMyGraph; j ++) {
        if (myGraph [LineIndex] [j] == 1) {
            ConnectedNodes [TreeWidth] = myGraph [0] [j];
            TreeWidth ++;
        }
    }
    for (int i = 0;
    i < NumVerticesOfMyGraph; i ++) {
        if (i < LineIndex) {
            for (int j = 0;
            j < NumVerticesOfMyGraph; j ++) {
                if (j < LineIndex) {
                    DecompositionedMatrix [i] [j] = myGraph [i] [j];
                } else if (j > LineIndex) {
                    DecompositionedMatrix [i] [j - 1] = myGraph [i] [j];
                }

            }
        } else if (i > LineIndex) {
            for (int j = 0;
            j < NumVerticesOfMyGraph; j ++) {
                if (j < LineIndex) {
                    DecompositionedMatrix [i - 1] [j] = myGraph [i] [j];
                } else if (j > LineIndex) {
                    DecompositionedMatrix [i - 1] [j - 1] = myGraph [i] [j];
                }

            }
        }

    }
    for (int k = 0;
    k < TreeWidth; k ++) {
        for (int i = 0;
        i < DecompositionedMatrix.length; i ++) {
            if (DecompositionedMatrix [i] [0] == ConnectedNodes [k]) {
                for (int l = 0;
                l < TreeWidth; l ++) {
                    for (int j = 0;
                    j < DecompositionedMatrix.length; j ++) {
                        if (DecompositionedMatrix [0] [j] == ConnectedNodes [l]) {
                            DecompositionedMatrix [i] [j] = 1;
                        }
                    }
                }
            }
        }
    }
    for (int i = 1;
    i < DecompositionedMatrix.length; i ++) {
        DecompositionedMatrix [i] [i] = 0;
        for (int j = 1;
        j < DecompositionedMatrix.length; j ++) {
            DecompositionedMatrix [i] [j] = DecompositionedMatrix [j] [i];
        }
    }
    for (int l = 1;
    l < SolutionVector.length; l ++) {
        NextSolutionVector [l - 1] = SolutionVector [l];
    }
    if (NextSolutionVector.length > 1) {
        DeeperTreeWidth = CalculateTreeWidth (DecompositionedMatrix, NextSolutionVector, zaehler + 1);
        if (TreeWidth < DeeperTreeWidth) {
            TreeWidth = DeeperTreeWidth;
        }
    }
    return TreeWidth;
}
",19332616,"public double [] [] getFSDistances () {
    int size = getMatrix ().size ();
    double [] [] distances;
    try {
        distances = new double [size] [size];
        for (int i = 0;
        i < size; i ++) {
            double distii = get (i, i);
            for (int j = i;
            j < size; j ++) {
                distances [i] [j] = Math.sqrt (distii + get (j, j) - 2 * get (i, j));
                distances [j] [i] = distances [i] [j];
            }
        }
    } catch (OutOfMemoryError e) {
        distances = null;
        System.err.println (""Not enough memory for distances!"");
        System.gc ();
    }
    return distances;
}
",Transpose a Matrix.,Type-3 (WT3/4),TRUE
3076854,"public static byte [] SHA1 (String text) throws NoSuchAlgorithmException, UnsupportedEncodingException {
    MessageDigest md;
    md = MessageDigest.getInstance (""SHA-1"");
    byte [] sha1hash = new byte [40];
    md.update (text.getBytes (""iso-8859-1""), 0, text.length ());
    sha1hash = md.digest ();
    return sha1hash;
}
",6176440,"public static String encrypt (String password, String algorithm, byte [] salt) {
    StringBuffer buffer = new StringBuffer ();
    MessageDigest digest = null;
    int size = 0;
    if (""CRYPT"".equalsIgnoreCase (algorithm)) {
        throw new InternalError (""Not implemented"");
    } else if (""SHA"".equalsIgnoreCase (algorithm) || ""SSHA"".equalsIgnoreCase (algorithm)) {
        size = 20;
        if (salt != null && salt.length > 0) {
            buffer.append (""{SSHA}"");
        } else {
            buffer.append (""{SHA}"");
        }
        try {
            digest = MessageDigest.getInstance (""SHA-1"");
        } catch (NoSuchAlgorithmException e) {
            throw new InternalError (""Invalid algorithm"");
        }
    } else if (""MD5"".equalsIgnoreCase (algorithm) || ""SMD5"".equalsIgnoreCase (algorithm)) {
        size = 16;
        if (salt != null && salt.length > 0) {
            buffer.append (""{SMD5}"");
        } else {
            buffer.append (""{MD5}"");
        }
        try {
            digest = MessageDigest.getInstance (""MD5"");
        } catch (NoSuchAlgorithmException e) {
            throw new InternalError (""Invalid algorithm"");
        }
    }

    int outSize = size;
    digest.reset ();
    digest.update (password.getBytes ());
    if (salt != null && salt.length > 0) {
        digest.update (salt);
        outSize += salt.length;
    }
    byte [] out = new byte [outSize];
    System.arraycopy (digest.digest (), 0, out, 0, size);
    if (salt != null && salt.length > 0) {
        System.arraycopy (salt, 0, out, size, salt.length);
    }
    buffer.append (Base64.encode (out));
    return buffer.toString ();
}
",Secure Hash,Type-3 (WT3/4),TRUE
951388,"public static void zipFile (String file, String entry) throws IOException {
    FileInputStream in = new FileInputStream (file);
    ZipOutputStream out = new ZipOutputStream (new FileOutputStream (file + "".zip""));
    out.putNextEntry (new ZipEntry (entry));
    byte [] buffer = new byte [4096];
    int bytes_read;
    while ((bytes_read = in.read (buffer)) != - 1) out.write (buffer, 0, bytes_read);

    in.close ();
    out.closeEntry ();
    out.close ();
    File fin = new File (file);
    fin.delete ();
}
",11915880,"private static void cut () {
    File inputFile = new File (inputFileName);
    BufferedReader in = null;
    try {
        in = new BufferedReader (new InputStreamReader (new FileInputStream (inputFile), inputCharSet));
    } catch (FileNotFoundException e) {
        System.err.print (""Invalid File Name!"");
        System.err.flush ();
        System.exit (1);
    } catch (UnsupportedEncodingException e) {
        System.err.print (""Invalid Char Set Name!"");
        System.err.flush ();
        System.exit (1);
    }
    switch (cutMode) {
        case charMode :
            {
                int outputFileIndex = 1;
                char [] readBuf = new char [charPerFile];
                while (true) {
                    int readCount = 0;
                    try {
                        readCount = in.read (readBuf);
                    } catch (IOException e) {
                        System.err.println (""Read IO Error!"");
                        System.err.flush ();
                        System.exit (1);
                    }
                    if (- 1 == readCount) break;
                    else {
                        try {
                            int ppos = inputFileName.lastIndexOf (""."");
                            String prefixInputFileName = inputFileName.substring (0, ppos);
                            String postfixInputFileName = ""html"";
                            DecimalFormat outputFileIndexFormat = new DecimalFormat (""0000"");
                            File outputFile = new File (prefixInputFileName + ""-"" + outputFileIndexFormat.format (outputFileIndex) + ""."" + postfixInputFileName);
                            BufferedWriter out = new BufferedWriter (new OutputStreamWriter (new FileOutputStream (outputFile), outputCharSet));
                            out.write (readBuf, 0, readCount);
                            out.flush ();
                            out.close ();
                            outputFileIndex ++;
                        } catch (IOException e) {
                            System.err.println (""Write IO Error!"");
                            System.err.flush ();
                            System.exit (1);
                        }
                    }
                }
                break;
            } case lineMode :
            {
                boolean isFileEnd = false;
                int outputFileIndex = 1;
                while (! isFileEnd) {
                    try {
                        int ppos = inputFileName.lastIndexOf (""."");
                        String prefixInputFileName = inputFileName.substring (0, ppos);
                        String postfixInputFileName = inputFileName.substring (ppos + 1);
                        DecimalFormat outputFileIndexFormat = new DecimalFormat (""0000"");
                        File outputFile = new File (prefixInputFileName + outputFileIndexFormat.format (outputFileIndex) + ""."" + postfixInputFileName);
                        PrintStream out = new PrintStream (new FileOutputStream (outputFile), false, outputCharSet);
                        int p = 0;
                        while (p < linePerFile) {
                            String line = in.readLine ();
                            if (null == line) {
                                isFileEnd = true;
                                break;
                            }
                            out.println (line);
                            ++ p;
                        }
                        out.flush ();
                        out.close ();
                    } catch (IOException e) {
                        System.err.println (""Write IO Error!"");
                        System.err.flush ();
                        System.exit (1);
                    }
                    ++ outputFileIndex;
                }
                break;
            } case htmlMode :
            {
                boolean isFileEnd = false;
                int outputFileIndex = 1;
                int ppos = inputFileName.lastIndexOf (""."");
                String prefixInputFileName = inputFileName.substring (0, ppos);
                String postfixInputFileName = ""html"";
                DecimalFormat df = new DecimalFormat (""0000"");
                while (! isFileEnd) {
                    try {
                        File outputFile = new File (prefixInputFileName + ""-"" + df.format (outputFileIndex) + ""."" + postfixInputFileName);
                        PrintStream out = new PrintStream (new FileOutputStream (outputFile), false, outputCharSet);
                        out.println (""<html><head><title>"" + prefixInputFileName + ""-"" + df.format (outputFileIndex) + ""</title>"" + ""<meta http-equiv=\""Content-Type\"""" + "" content=\""text/html; "" + ""charset="" + outputCharSet + ""\"" />"" + ""<link rel =\""stylesheet\"" "" + ""type=\""text/css\"" "" + ""href=\""stylesheet.css\"" />"" + ""</head><body><div id=\""content\"">"");
                        int p = 0;
                        while (p < pPerFile) {
                            String line = in.readLine ();
                            if (null == line) {
                                isFileEnd = true;
                                break;
                            }
                            if (line.length () > 0) out.println (""<p>"" + line + ""</p>"");

                            ++ p;
                        }
                        out.println (""</div><a href=\"""" + prefixInputFileName + ""-"" + df.format (outputFileIndex + 1) + ""."" + postfixInputFileName + ""\"">NEXT</a></body></html>"");
                        out.flush ();
                        out.close ();
                    } catch (IOException e) {
                        System.err.println (""Write IO Error!"");
                        System.err.flush ();
                        System.exit (1);
                    }
                    ++ outputFileIndex;
                }
                try {
                    File indexFile = new File (""index.html"");
                    PrintStream out = new PrintStream (new FileOutputStream (indexFile), false, outputCharSet);
                    out.println (""<html><head><title>"" + ""Index"" + ""</title>"" + ""<meta http-equiv=\""Content-Type\"""" + "" content=\""text/html; "" + ""charset="" + outputCharSet + ""\"" />"" + ""<link rel =\""stylesheet\"" "" + ""type=\""text/css\"" "" + ""href=\""stylesheet.css\"" />"" + ""</head><body><h2>"" + htmlTitle + ""</h2><div id=\""content\""><ul>"");
                    for (int i = 1;
                    i < outputFileIndex; i ++) {
                        out.println (""<li><a href=\"""" + prefixInputFileName + ""-"" + df.format (i) + ""."" + postfixInputFileName + ""\"">"" + df.format (i) + ""</a></li>"");
                    }
                    out.println (""</ul></body></html>"");
                    out.flush ();
                    out.close ();
                } catch (IOException e) {
                    System.err.println (""Write IO Error!"");
                    System.err.flush ();
                    System.exit (1);
                }
                break;
            }}
}
",Copy File,Type-3 (WT3/4),TRUE
2049240,"private void writeInfos () throws IOException {
    zos.putNextEntry (new ZipEntry (""info.bin""));
    outFile = new DataOutputStream (zos);
    outFile.writeInt (VERSION);
    outFile.writeInt (MINORVERSION);
    outFile.writeDouble (intervall_s);
    zos.closeEntry ();
}
",4078781,"public static boolean zipFiles (File output, File...input) {
    if (output == null || input == null || input.length == 0) {
        return false;
    }
    if (! deleteFile (output)) {
        return false;
    }
    byte [] buf = new byte [1024];
    ZipOutputStream out = null;
    try {
        out = new ZipOutputStream (new FileOutputStream (output));
        for (int i = 0;
        i < input.length; i ++) {
            FileInputStream in = null;
            try {
                in = new FileInputStream (input [i]);
                out.putNextEntry (new ZipEntry (input [i].getName ()));
                int len;
                while ((len = in.read (buf)) > 0) {
                    out.write (buf, 0, len);
                }
                out.closeEntry ();
            } finally {
                FileUtil.close (in);
            }
        }
    } catch (IOException ex) {
        ShowDownLog.getInstance ().logError (ex.getLocalizedMessage (), ex);
        return false;
    } finally {
        FileUtil.close (out);
    }
    return true;
}
",Zip Files,Type-3 (WT3/4),FALSE
12821749,"public static void fastBackup (File file) {
    FileChannel in = null;
    FileChannel out = null;
    FileInputStream fin = null;
    FileOutputStream fout = null;
    try {
        in = (fin = new FileInputStream (file)).getChannel ();
        out = (fout = new FileOutputStream (file.getAbsolutePath () + "".bak"")).getChannel ();
        in.transferTo (0, in.size (), out);
    } catch (IOException e) {
        Logging.getErrorLog ().reportError (""Fast backup failure ("" + file.getAbsolutePath () + ""): "" + e.getMessage ());
    } finally {
        if (fin != null) {
            try {
                fin.close ();
            } catch (IOException e) {
                Logging.getErrorLog ().reportException (""Failed to close file input stream"", e);
            }
        }
        if (fout != null) {
            try {
                fout.close ();
            } catch (IOException e) {
                Logging.getErrorLog ().reportException (""Failed to close file output stream"", e);
            }
        }
        if (in != null) {
            try {
                in.close ();
            } catch (IOException e) {
                Logging.getErrorLog ().reportException (""Failed to close file channel"", e);
            }
        }
        if (out != null) {
            try {
                out.close ();
            } catch (IOException e) {
                Logging.getErrorLog ().reportException (""Failed to close file channel"", e);
            }
        }
    }
}
",18034383,"public static File copy (String inFileName, String outFileName) throws IOException {
    File inputFile = new File (inFileName);
    File outputFile = new File (outFileName);
    FileReader in = new FileReader (inputFile);
    FileWriter out = new FileWriter (outputFile);
    int c;
    while ((c = in.read ()) != - 1) out.write (c);

    in.close ();
    out.close ();
    return outputFile;
}
",Copy File,Type-3 (WT3/4),TRUE
891055,"@Override
public void run () {
    final Random r = new Random ();
    final Counter counter = new Counter (""TRANSMIT"", plotter);
    counter.start ();
    try {
        final DataOutputStream dos = new DataOutputStream (new BufferedOutputStream (s.getOutputStream ()));
        while (! Thread.interrupted ()) {
            if (! running.get ()) {
                Thread.sleep (1000);
                continue;
            }
            final int packetSize = r.nextInt (8192) + 2048;
            final byte [] packet = new byte [packetSize];
            r.nextBytes (packet);
            final CRC32 crc = new CRC32 ();
            crc.update (packet);
            dos.writeInt (packetSize);
            counter.addBytes (INTEGER_BYTES);
            dos.write (packet);
            counter.addBytes (packetSize);
            dos.writeLong (crc.getValue ());
            counter.addBytes (CRC_BYTES);
            dos.flush ();
        }
    } catch (InterruptedException e) {
        System.out.println (""Transmitter thread interrupted!"");
    } catch (Exception e) {
        System.err.println (""Unexpected error in transmitter thread: "" + e.getMessage ());
    } finally {
        abortLatch.countDown ();
        counter.interrupt ();
    }
}
",15357608,"private void cRC32Test (byte [] values, long expected) {
    CRC32 crc = new CRC32 ();
    crc.update (values);
    assertEquals (crc.getValue (), expected);
    crc.reset ();
    for (int i = 0;
    i < values.length; i ++) {
        crc.update (values [i]);
    }
    assertEquals (crc.getValue (), expected);
}
",CRC32 File Checksum,Type-3 (WT3/4),FALSE
742784,"public boolean create () {
    DirectoryManager d = new DirectoryManager (dirSource);
    Vector < String > filenames = new Vector < String > ();
    d.getAllMyFileNames (filenames, true, false);
    byte [] buf = new byte [1024];
    try {
        ZipOutputStream out = null;
        BufferedOutputStream outStream = null;
        SevenZip.Compression.LZMA.Encoder encoder = null;
        boolean eos = false;
        if (! useLZMA) {
            out = new ZipOutputStream (new FileOutputStream (zip));
        } else {
            outStream = new BufferedOutputStream (new FileOutputStream (new File (zip)));
            encoder = new SevenZip.Compression.LZMA.Encoder ();
            encoder.SetAlgorithm (2);
            encoder.SetDictionarySize (1 << 21);
            encoder.SeNumFastBytes (128);
            encoder.SetMatchFinder (1);
            encoder.SetLcLpPb (3, 0, 2);
            encoder.SetEndMarkerMode (eos);
            encoder.WriteCoderProperties (outStream);
        }
        for (int i = 0;
        i < filenames.size (); i ++) {
            myMaster.writeOnLog (""processing : "" + filenames.elementAt (i) + "" to create "" + filenames.elementAt (i).replace (d.getDirectory (), """"));
            if (! useLZMA) {
                FileInputStream in = new FileInputStream (filenames.elementAt (i));
                out.putNextEntry (new ZipEntry (filenames.elementAt (i).replace (d.getDirectory (), """")));
                int len;
                while ((len = in.read (buf)) > 0) {
                    out.write (buf, 0, len);
                }
                out.closeEntry ();
                in.close ();
            } else {
                File inFile = new File (filenames.elementAt (i));
                BufferedInputStream inStream = new BufferedInputStream (new FileInputStream (new File (filenames.elementAt (i))));
                long fileSize;
                if (eos) fileSize = - 1;
                else fileSize = inFile.length ();

                for (int j = 0;
                j < 8; j ++) outStream.write ((int) (fileSize>>> (8 * j)) & 0xFF);

                encoder.Code (inStream, outStream, - 1, - 1, null);
                inStream.close ();
            }
            myMaster.setProgress (1);
        }
        if (! useLZMA) out.close ();
        else {
            outStream.flush ();
            outStream.close ();
        }
    } catch (IOException e) {
        myMaster.writeOnLog (""error while creating zip file : "" + e);
        return false;
    }
    return true;
}
",1312065,"public void addFile (ZipOutputStream out, String filename) {
    try {
        byte [] buf = new byte [1024];
        String filePath = projHandler.getProjectPath () + File.separator + filename;
        File file = new File (filePath);
        if (file.exists ()) {
            FileInputStream fis = new FileInputStream (filePath);
            out.putNextEntry (new ZipEntry (filename));
            int len;
            while ((len = fis.read (buf)) > 0) {
                out.write (buf, 0, len);
            }
            out.closeEntry ();
            fis.close ();
        }
    } catch (Exception e) {
        e.printStackTrace ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
418257,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",1467288,"private static String addFile (File ff, ZipOutputStream zipOutPic, String filename) throws Exception {
    FileInputStream file = new FileInputStream (ff);
    String ext = getFileExt (ff.getName ());
    if (! ext.equals ("""")) {
        ext = ""."" + ext;
    }
    int randomString = ((int) (Math.random () * 1000000));
    while (randomList.contains (randomString)) {
        randomString = ((int) (Math.random () * 1000000));
    }
    randomList.add (randomString);
    String newFilename = filename == null ? randomString + ext : filename;
    ZipEntry entryPic = new ZipEntry (newFilename);
    zipOutPic.putNextEntry (entryPic);
    byte [] buf = new byte [1024];
    int len;
    while ((len = file.read (buf)) > 0) {
        zipOutPic.write (buf, 0, len);
    }
    zipOutPic.closeEntry ();
    return newFilename;
}
",Zip Files,Type-3 (WT3/4),FALSE
778875,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",20967084,"private void writeIntoZip (ZipOutputStream output, String name, InputStream input) throws Exception {
    output.putNextEntry (new ZipEntry (name));
    int size = 0;
    byte [] buffer = new byte [1024];
    while ((size = input.read (buffer, 0, buffer.length)) > 0) {
        output.write (buffer, 0, size);
    }
    output.closeEntry ();
    input.close ();
}
",Zip Files,Type-3 (WT3/4),FALSE
11322590,"private static void addFileToZip (String path, String srcFile, ZipOutputStream zip) throws Exception {
    File folder = new File (srcFile);
    if (folder.isDirectory ()) {
        addFolderToZip (path, srcFile, zip);
    } else {
        byte [] buf = new byte [1024];
        int len;
        FileInputStream in = new FileInputStream (srcFile);
        zip.putNextEntry (new ZipEntry (path + ""\\"" + folder.getName ()));
        while ((len = in.read (buf)) > 0) {
            zip.write (buf, 0, len);
        }
    }
}
",14138100,"public static void insertModuleinfo (ZipOutputStream dest, ModuleInfo info) throws IOException {
    ZipEntry zse = new ZipEntry (ModuleInfo.MODULEINFO_RAK);
    dest.putNextEntry (zse);
    info.write (dest);
    dest.flush ();
}
",Zip Files,Type-3 (WT3/4),TRUE
1446727,"private void backupDiskFile (ZipOutputStream out, String fileName, DiskFile file) throws SQLException, IOException {
    Database db = session.getDatabase ();
    fileName = FileUtils.getFileName (fileName);
    out.putNextEntry (new ZipEntry (fileName));
    int pos = - 1;
    int max = file.getReadCount ();
    while (true) {
        pos = file.copyDirect (pos, out);
        if (pos < 0) {
            break;
        }
        db.setProgress (DatabaseEventListener.STATE_BACKUP_FILE, fileName, pos, max);
    }
    out.closeEntry ();
}
",10062068,"private void addToArchive (ZipOutputStream stream, File file, FileFilter filter, String entryName, int recurseDepth) throws IOException {
    if (file.exists ()) {
        if (file.isDirectory ()) {
            File [] ls = file.listFiles (filter);
            if (ls.length == 0) {
                if (archiveEntryList_.contains (entryName + ""/"")) {
                    System.err.println (""  warning: duplicate entry: "" + entryName + ""/"" + "". Skipping."");
                } else {
                    System.out.println (""  "" + file);
                    ZipEntry newEntry = new ZipEntry (entryName + ""/"");
                    stream.putNextEntry (newEntry);
                    stream.closeEntry ();
                    archiveEntryList_.add (entryName + ""/"");
                }
            }
            for (int i = 0;
            i < ls.length; i ++) {
                String ename = ls [i].getAbsolutePath ();
                ename = entryName + ename.substring (file.getAbsolutePath ().length ());
                ename = convertToGenericPath (ename);
                if (ename.startsWith (""/"")) ename = ename.substring (1);

                if (recurseDepth > 0) addToArchive (stream, ls [i], filter, ename, recurseDepth - 1);

            }
        } else if (archiveEntryList_.contains (entryName)) {
            System.err.println (""  warning: duplicate entry: "" + entryName + "". Skipping."");
        } else {
            System.out.println (""  "" + file);
            archivecount_ ++;
            ZipEntry newEntry = new ZipEntry (entryName);
            stream.putNextEntry (newEntry);
            FileInputStream in = new FileInputStream (file);
            byte [] buf = new byte [2048];
            int read = in.read (buf, 0, buf.length);
            while (read > 0) {
                stream.write (buf, 0, read);
                read = in.read (buf, 0, buf.length);
            }
            in.close ();
            stream.closeEntry ();
            archiveEntryList_.add (entryName);
        }

    } else {
        System.err.println (""  error: file "" + file + "" does not exist. Skipping."");
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
7556871,"private static byte [] createMD5 (String seed) throws UnsupportedEncodingException, NoSuchAlgorithmException {
    MessageDigest md5 = MessageDigest.getInstance (""MD5"");
    md5.reset ();
    md5.update (seed.getBytes (""UTF-8""));
    return md5.digest ();
}
",19474501,"private void getRandomGUID (boolean secure) {
    MessageDigest md5 = null;
    StringBuffer sbValueBeforeMD5 = new StringBuffer ();
    try {
        md5 = MessageDigest.getInstance (""MD5"");
    } catch (NoSuchAlgorithmException e) {
        System.out.println (""Error: "" + e);
    }
    try {
        long time = System.currentTimeMillis ();
        long rand = 0;
        if (secure) {
            rand = mySecureRand.nextLong ();
        } else {
            rand = myRand.nextLong ();
        }
        sbValueBeforeMD5.append (s_id);
        sbValueBeforeMD5.append ("":"");
        sbValueBeforeMD5.append (Long.toString (time));
        sbValueBeforeMD5.append ("":"");
        sbValueBeforeMD5.append (Long.toString (rand));
        valueBeforeMD5 = sbValueBeforeMD5.toString ();
        md5.update (valueBeforeMD5.getBytes ());
        byte [] array = md5.digest ();
        StringBuffer sb = new StringBuffer ();
        for (int j = 0;
        j < array.length; ++ j) {
            int b = array [j] & 0xFF;
            if (b < 0x10) sb.append ('0');

            sb.append (Integer.toHexString (b));
        }
        valueAfterMD5 = sb.toString ();
    } catch (Exception e) {
        System.out.println (""Error:"" + e);
    }
}
",Secure Hash,Type-3 (WT3/4),TRUE
469376,"protected void flatten (File dir) {
    assert dir.isDirectory ();
    File [] files = dir.listFiles ();
    for (int i = 0;
    i < files.length; i ++) {
        File subfile = files [i];
        if (subfile.isFile ()) {
            continue;
        } else {
            flatten (subfile);
            File [] subfiles = subfile.listFiles ();
            for (int j = 0;
            j < subfiles.length; j ++) {
                File f = subfiles [j];
                File temp = new File (subfile.getParent () + '\\' + subfile.getName () + '_' + f.getName ());
                if (f.renameTo (temp) == false) {
                    throw new RuntimeException (""Cannot rename: "" + f.toString ());
                } else {
                    System.out.println (f.toString () + "". Rename OK!"");
                }
            }
            if (subfile.delete () == false) {
                throw new RuntimeException (""Cannot delete: "" + subfile.toString ());
            }
        }
    }
}
",662161,"public static boolean deleteDirectory (File path) {
    if (path.exists ()) {
        File [] files = path.listFiles ();
        for (int i = 0;
        i < files.length; i ++) {
            if (files [i].isDirectory ()) {
                deleteDirectory (files [i]);
            } else {
                files [i].delete ();
            }
        }
    }
    return (path.delete ());
}
",Delete Folder and Contents,Type-3 (WT3/4),FALSE
13374130,"private void zipLog (InfoRolling info) {
    boolean zipped = false;
    File [] logFiles = info.getFiles ();
    try {
        GregorianCalendar gc = (GregorianCalendar) GregorianCalendar.getInstance ();
        gc.roll (Calendar.DAY_OF_MONTH, info.getBackRolling ());
        final String prefixFileName = logFileName.substring (0, logFileName.indexOf ("".""));
        final String date = sdf.format (gc.getTime ());
        String tarName = new StringBuffer (prefixFileName).append (date).append ("".tar"").toString ();
        String gzipFileName = new StringBuffer (tarName).append ("".zip"").toString ();
        String tarPath = new StringBuffer (logDir).append (File.separator).append (tarName).toString ();
        TarArchive ta = new TarArchive (new FileOutputStream (tarPath));
        for (int i = 0;
        i < logFiles.length; i ++) {
            File file = logFiles [i];
            TarEntry te = new TarEntry (file);
            ta.writeEntry (te, true);
        }
        ta.closeArchive ();
        ZipEntry zipEntry = new ZipEntry (tarName);
        zipEntry.setMethod (ZipEntry.DEFLATED);
        ZipOutputStream zout = new ZipOutputStream (new FileOutputStream (new StringBuffer (logDir).append (File.separator).append (gzipFileName).toString ()));
        zout.putNextEntry (zipEntry);
        InputStream in = new FileInputStream (tarPath);
        byte [] buffer = new byte [2048];
        int ch = 0;
        while ((ch = in.read (buffer)) >= 0) {
            zout.write (buffer, 0, ch);
        }
        zout.flush ();
        zout.close ();
        in.close ();
        logFiles = new File (getFile ().substring (0, getFile ().lastIndexOf (File.separator))).listFiles (new FileFilter () {
            public boolean accept (File file) {
                return file.getName ().endsWith ("".tar"");
            }}

        );
        for (int i = 0;
        i < logFiles.length; i ++) {
            File file = logFiles [i];
            System.out.println (""cancello : "" + file.getAbsolutePath () + "" : "" + file.delete ());
        }
        logFiles = new File (getFile ().substring (0, getFile ().lastIndexOf (File.separator))).listFiles (new FileFilter () {
            public boolean accept (File file) {
                return file.getName ().indexOf (prefixFileName + "".log"" + date) != - 1 && ! file.getName ().endsWith ("".zip"");
            }}

        );
        for (int i = 0;
        i < logFiles.length; i ++) {
            File file = logFiles [i];
            System.out.println (""cancello : "" + file.getAbsolutePath () + "" : "" + file.delete ());
        }
        zipped = true;
    } catch (FileNotFoundException ex) {
        LogLog.error (""Filenotfound: "" + ex.getMessage (), ex);
    } catch (IOException ex) {
        LogLog.error (""IOException: "" + ex.getMessage (), ex);
    } finally {
        if (zipped) {
            for (int i = 0;
            i < logFiles.length; i ++) {
                File file = logFiles [i];
                file.delete ();
            }
        }
    }
}
",14548451,"private static final void zipEntry (File sourceFile, String sourcePath, ZipOutputStream zos) throws IOException {
    if (sourceFile.isDirectory ()) {
        if (sourceFile.getName ().equalsIgnoreCase ("".metadata"")) {
            return;
        }
        File [] fileArray = sourceFile.listFiles ();
        for (int i = 0;
        i < fileArray.length; i ++) {
            zipEntry (fileArray [i], sourcePath, zos);
        }
    } else {
        BufferedInputStream bis = null;
        String sFilePath = sourceFile.getPath ();
        String zipEntryName = sFilePath.substring (sourcePath.length () + 1, sFilePath.length ());
        bis = new BufferedInputStream (new FileInputStream (sourceFile));
        ZipEntry zentry = new ZipEntry (zipEntryName);
        zentry.setTime (sourceFile.lastModified ());
        zos.putNextEntry (zentry);
        byte [] buffer = new byte [BUFFER_SIZE];
        int cnt = 0;
        while ((cnt = bis.read (buffer, 0, BUFFER_SIZE)) != - 1) {
            zos.write (buffer, 0, cnt);
        }
        zos.closeEntry ();
        bis.close ();
    }
}
",Zip Files,Type-3 (WT3/4),TRUE
469518,"public synchronized void writeFile (String filename) throws IOException {
    int amount;
    byte buffer [] = new byte [4096];
    File f = new File (filename);
    FileInputStream in = new FileInputStream (f);
    putNextEntry (new ZipEntry (f.getName ()));
    while ((amount = in.read (buffer)) != - 1) write (buffer, 0, amount);

    closeEntry ();
    in.close ();
}
",1719182,"public void actionPerformed (ActionEvent evt) {
    Object src = evt.getSource ();
    if (src == scanForImages) {
        JFileChooser chooser = (JFileChooser) objects.getObject (JFileChooser.class);
        if (chooser.showOpenDialog (this) != JFileChooser.APPROVE_OPTION) {
            return;
        }
        File dir = chooser.getSelectedFile ();
        if (! dir.isDirectory ()) {
            dir = dir.getParentFile ();
        }
        resyncImageSelection (dir);
    } else if (src == createPC) {
        try {
            File floppyImage = floppyDisk.getSelectedFile ();
            File hardImage = hardDisk.getSelectedFile ();
            File cdImage = cdrom.getSelectedFile ();
            DriveSet.BootType bootType;
            if (floppyDisk.isBootDevice ()) {
                if (! floppyImage.exists ()) {
                    alert (""Floppy Image: "" + floppyImage + "" does not exist"", ""Boot"", JOptionPane.ERROR_MESSAGE);
                    return;
                }
                bootType = DriveSet.BootType.FLOPPY;
            } else if (hardDisk.isBootDevice ()) {
                if (! hardImage.exists ()) {
                    alert (""Hard disk Image: "" + hardImage + "" does not exist"", ""Boot"", JOptionPane.ERROR_MESSAGE);
                    return;
                }
                bootType = DriveSet.BootType.HARD_DRIVE;
            } else {
                if (! cdImage.exists ()) {
                    alert (""CD Image: "" + cdImage + "" does not exist"", ""Boot"", JOptionPane.ERROR_MESSAGE);
                    return;
                }
                bootType = DriveSet.BootType.CDROM;
            }

            String [] args;
            int argc = 0;
            if (floppyImage != null) {
                argc += 2;
            }
            if (hardImage != null) {
                argc += 2;
            }
            if (cdImage != null) {
                argc += 2;
            }
            if (argc > 2) {
                argc += 2;
            }
            args = new String [argc];
            int pos = 0;
            if (floppyImage != null) {
                args [pos ++] = ""-fda"";
                args [pos ++] = floppyImage.getAbsolutePath ();
            }
            if (hardImage != null) {
                args [pos ++] = ""-hda"";
                args [pos ++] = hardImage.getAbsolutePath ();
            }
            if (cdImage != null) {
                args [pos ++] = ""-cdrom"";
                args [pos ++] = cdImage.getAbsolutePath ();
            }
            if (pos <= (argc - 2)) {
                args [pos ++] = ""-boot"";
                if (bootType == DriveSet.BootType.HARD_DRIVE) {
                    args [pos ++] = ""hda"";
                } else if (bootType == DriveSet.BootType.CDROM) {
                    args [pos ++] = ""cdrom"";
                } else {
                    args [pos ++] = ""fda"";
                }

            }
            instance.createPC (args);
            resyncImageSelection (new File (System.getProperty (""user.dir"")));
        } catch (Exception e) {
            alert (""Failed to create PC: "" + e, ""Boot"", JOptionPane.ERROR_MESSAGE);
        }
    } else if (src == loadSnapshot) {
        runMenu.stop ();
        JFileChooser fc = new JFileChooser ();
        try {
            BufferedReader in = new BufferedReader (new FileReader (""prefs.txt""));
            String path = in.readLine ();
            in.close ();
            if (path != null) {
                File f = new File (path);
                if (f.isDirectory ()) {
                    fc.setCurrentDirectory (f);
                }
            }
        } catch (Exception e) {
        }
        int returnVal = fc.showDialog (this, ""Load JPC Snapshot"");
        File file = fc.getSelectedFile ();
        try {
            if (file != null) {
                BufferedWriter out = new BufferedWriter (new FileWriter (""prefs.txt""));
                out.write (file.getPath ());
                out.close ();
            }
        } catch (Exception e) {
            e.printStackTrace ();
        }
        if (returnVal == 0) {
            try {
                System.out.println (""Loading a snapshot of JPC"");
                ZipInputStream zin = new ZipInputStream (new FileInputStream (file));
                zin.getNextEntry ();
                ((PC) objects.getObject (PC.class)).loadState (zin);
                zin.closeEntry ();
                ((PCMonitorFrame) objects.getObject (PCMonitorFrame.class)).resizeDisplay ();
                zin.getNextEntry ();
                ((PCMonitorFrame) objects.getObject (PCMonitorFrame.class)).loadMonitorState (zin);
                zin.closeEntry ();
                zin.close ();
                System.out.println (""done"");
            } catch (IOException e) {
                e.printStackTrace ();
            }
        }
    } else if (src == saveSnapshot) {
        runMenu.stop ();
        JFileChooser fc = new JFileChooser ();
        try {
            BufferedReader in = new BufferedReader (new FileReader (""prefs.txt""));
            String path = in.readLine ();
            in.close ();
            if (path != null) {
                File f = new File (path);
                if (f.isDirectory ()) {
                    fc.setCurrentDirectory (f);
                }
            }
        } catch (Exception e) {
        }
        int returnVal = fc.showDialog (this, ""Save JPC Snapshot"");
        File file = fc.getSelectedFile ();
        try {
            if (file != null) {
                BufferedWriter out = new BufferedWriter (new FileWriter (""prefs.txt""));
                out.write (file.getPath ());
                out.close ();
            }
        } catch (Exception e) {
            e.printStackTrace ();
        }
        if (returnVal == 0) {
            try {
                ZipOutputStream zip = new ZipOutputStream (new FileOutputStream (file));
                zip.putNextEntry (new ZipEntry (""pc""));
                ((PC) objects.getObject (PC.class)).saveState (zip);
                zip.closeEntry ();
                zip.putNextEntry (new ZipEntry (""monitor""));
                ((PCMonitorFrame) objects.getObject (PCMonitorFrame.class)).saveState (zip);
                zip.closeEntry ();
                zip.finish ();
                zip.close ();
            } catch (IOException e) {
                e.printStackTrace ();
            }
        }
    } else if (src == processorFrame) {
        ProcessorFrame pf = (ProcessorFrame) objects.getObject (ProcessorFrame.class);
        if (pf != null) {
            bringToFront (pf);
        } else {
            pf = new ProcessorFrame ();
            addInternalFrame (desktop, 10, 10, pf);
        }
    } else if (src == physicalMemoryViewer) {
        MemoryViewer mv = (MemoryViewer) objects.getObject (MemoryViewer.class);
        if (mv != null) {
            bringToFront (mv);
        } else {
            mv = new MemoryViewer (""Physical Memory"");
            addInternalFrame (desktop, 360, 50, mv);
        }
    } else if (src == linearMemoryViewer) {
        LinearMemoryViewer lmv = (LinearMemoryViewer) objects.getObject (LinearMemoryViewer.class);
        if (lmv != null) {
            bringToFront (lmv);
        } else {
            lmv = new LinearMemoryViewer (""Linear Memory"");
            addInternalFrame (desktop, 360, 50, lmv);
        }
    } else if (src == breakpoints) {
        BreakpointsFrame bp = (BreakpointsFrame) objects.getObject (BreakpointsFrame.class);
        if (bp != null) {
            bringToFront (bp);
        } else {
            bp = new BreakpointsFrame ();
            addInternalFrame (desktop, 550, 360, bp);
        }
    } else if (src == watchpoints) {
        WatchpointsFrame wp = (WatchpointsFrame) objects.getObject (WatchpointsFrame.class);
        if (wp != null) {
            bringToFront (wp);
        } else {
            wp = new WatchpointsFrame ();
            addInternalFrame (desktop, 550, 360, wp);
        }
    } else if (src == opcodeFrame) {
        OpcodeFrame op = (OpcodeFrame) objects.getObject (OpcodeFrame.class);
        if (op != null) {
            bringToFront (op);
        } else {
            op = new OpcodeFrame ();
            addInternalFrame (desktop, 100, 200, op);
        }
    } else if (src == traceFrame) {
        ExecutionTraceFrame tr = (ExecutionTraceFrame) objects.getObject (ExecutionTraceFrame.class);
        if (tr != null) {
            bringToFront (tr);
        } else {
            tr = new ExecutionTraceFrame ();
            addInternalFrame (desktop, 30, 100, tr);
        }
    } else if (src == monitor) {
        PCMonitorFrame m = (PCMonitorFrame) objects.getObject (PCMonitorFrame.class);
        if (m != null) {
            bringToFront (m);
        } else {
            m = new PCMonitorFrame ();
            addInternalFrame (desktop, 30, 30, m);
        }
    }

    refresh ();
}
",Zip Files,Type-3 (WT3/4),FALSE
9781386,"public void run () {
    root.setCursor (Cursor.getPredefinedCursor (3));
    try {
        tempArchiveFile = File.createTempFile (""JZip"", "".zip"");
        if (table.getRowCount () != delRows.length) {
            stream = new FileOutputStream (tempArchiveFile);
            out = new ZipOutputStream (stream);
            boolean aflag [] = new boolean [table.getRowCount ()];
            for (int i = 0;
            i < table.getRowCount (); i ++) {
                aflag [i] = false;
            }
            for (int j = 0;
            j < delRows.length; j ++) {
                aflag [delRows [j]] = true;
            }
            ZipFile zipfile = new ZipFile (archiveFile);
            for (int k = 0;
            k < table.getRowCount (); k ++) {
                if (! aflag [k]) {
                    Object obj = ziptm.getRealValueAt (k, 6);
                    String s1 = ziptm.getRealValueAt (k, 0).toString ();
                    String s2 = s1;
                    String s3 = """";
                    if (obj != null) {
                        String s4 = obj.toString ();
                        s2 = s4 + s1;
                    }
                    ZipEntry zipentry = zipfile.getEntry (s2.replace (File.separatorChar, '/'));
                    if (zipentry == null) {
                        System.out.println (""The entry with name<"" + s2 + ""> is null"");
                    } else {
                        InputStream inputstream = zipfile.getInputStream (zipentry);
                        out.putNextEntry (zipentry);
                        do {
                            int l = inputstream.read (buffer, 0, buffer.length);
                            if (l <= 0) {
                                break;
                            }
                            out.write (buffer, 0, l);
                        } while (true);
                        inputstream.close ();
                        out.closeEntry ();
                    }
                }
            }
            zipfile.close ();
            out.close ();
            stream.close ();
        }
        String s = archiveFile.getAbsolutePath ();
        archiveFile.delete ();
        tempArchiveFile.renameTo (new File (s));
        tempArchiveFile.getCanonicalPath ();
        openArchive (new File (s));
        table.clearSelection ();
        setStatus (""Totally "" + delRows.length + "" file(s) deleted from this archive!"");
    } catch (Exception exception) {
        exception.printStackTrace ();
        setStatus (""Error: "" + exception.getMessage ());
    }
    root.setCursor (Cursor.getPredefinedCursor (0));
    notifyAll ();
}
",12498692,"public void outputCitation (OutputStream outputStream, DataResourceAuditor resultsOutputter, String citationFileName, Locale locale, String hostUrl) throws IOException {
    if (outputStream instanceof ZipOutputStream) {
        ((ZipOutputStream) outputStream).putNextEntry (new ZipEntry (citationFileName));
    }
    Map < String, String > dataResources = resultsOutputter.getDataResources ();
    CitationCreator cc = new CitationCreator ();
    StringBuffer csb = cc.createCitation (dataResources, messageSource, locale, hostUrl + datasetBaseUrl);
    outputStream.write (csb.toString ().getBytes ());
    if (outputStream instanceof ZipOutputStream) {
        ((ZipOutputStream) outputStream).closeEntry ();
    }
}
",Zip Files,Type-3 (WT3/4),TRUE
9856200,"public static void copyFile (File srcFile, File destFolder) {
    try {
        File destFile = new File (destFolder, srcFile.getName ());
        if (destFile.exists ()) {
            throw new BuildException (""Could not copy "" + srcFile + "" to "" + destFolder + "" as "" + destFile + "" already exists"");
        }
        FileChannel srcChannel = null;
        FileChannel destChannel = null;
        try {
            srcChannel = new FileInputStream (srcFile).getChannel ();
            destChannel = new FileOutputStream (destFile).getChannel ();
            destChannel.transferFrom (srcChannel, 0, srcChannel.size ());
        } finally {
            if (srcChannel != null) {
                srcChannel.close ();
            }
            if (destChannel != null) {
                destChannel.close ();
            }
        }
        destFile.setLastModified ((srcFile.lastModified ()));
    } catch (IOException e) {
        throw new BuildException (""Could not copy "" + srcFile + "" to "" + destFolder + "": "" + e, e);
    }
}
",22556551,"private void copyOneFile (String oldPath, String newPath) {
    File copiedFile = new File (newPath);
    try {
        FileInputStream source = new FileInputStream (oldPath);
        FileOutputStream destination = new FileOutputStream (copiedFile);
        FileChannel sourceFileChannel = source.getChannel ();
        FileChannel destinationFileChannel = destination.getChannel ();
        long size = sourceFileChannel.size ();
        sourceFileChannel.transferTo (0, size, destinationFileChannel);
        source.close ();
        destination.close ();
    } catch (Exception exc) {
        exc.printStackTrace ();
    }
}
",Copy File,Type-3 (WT3/4),TRUE
1282820,"public TaskListPanel () {
    setLayout (new BorderLayout (0, 0));
    JScrollPane scrollPane = new JScrollPane ();
    table = new JTable ();
    table.addMouseListener (new MouseAdapter () {
        @Override
        public void mouseReleased (MouseEvent e) {
        }}

    );
    table.setModel (SMTSingleton.getSingletonInstance ().getCurrentSearch ().getTasks ());
    scrollPane.setViewportView (table);
    add (scrollPane, BorderLayout.CENTER);
    JPopupMenu popupMenu = new JPopupMenu ();
    addPopup (table, popupMenu);
    JMenuItem mntmPrintTaskAssignment = new JMenuItem (""Print Task Assignment Form"");
    mntmPrintTaskAssignment.addActionListener (new ActionListener () {
        public void actionPerformed (ActionEvent e) {
            int row = table.getSelectedRow ();
            String taskid = ((TaskList) table.getModel ()).getTaskAt (row).getIdentifier ();
            ((TaskList) table.getModel ()).getTaskAt (row).writeToPdf (taskid.replace (' ', '_') + ""_ICS-204a-OS"" + "".pdf"");
        }}

    );
    JMenuItem mntmEditTask = new JMenuItem (""Edit Task"");
    mntmEditTask.addActionListener (new ActionListener () {
        public void actionPerformed (ActionEvent e) {
            int row = table.getSelectedRow ();
            TaskDialog d = new TaskDialog (((TaskList) table.getModel ()).getTaskAt (row));
            d.setVisible (true);
        }}

    );
    popupMenu.add (mntmEditTask);
    popupMenu.add (mntmPrintTaskAssignment);
    popupMenu.addSeparator ();
    JMenuItem mntmPrintTaskAssignments = new JMenuItem (""Print All Task Assignment Forms"");
    mntmPrintTaskAssignments.addActionListener (new ActionListener () {
        public void actionPerformed (ActionEvent e) {
            Document document = new Document ();
            if (""A4"".equals (SMTSingleton.getSingletonInstance ().getProperties ().getProperties ().get (SMTProperties.KEY_PAPERSIZE))) {
                document.setPageSize (PageSize.A4);
            } else {
                document.setPageSize (PageSize.LETTER);
            }
            try {
                String filename = ""TaskList_ICS-204_with_Appendixes.pdf"";
                PdfWriter.getInstance (document, new FileOutputStream (filename));
                document.open ();
                TaskList tasks = ((TaskList) table.getModel ());
                tasks.writeToPdf (document);
                for (int i = 0;
                i < tasks.getRowCount (); i ++) {
                    tasks.getTaskAt (i).writeToPdf (document);
                }
                document.close ();
            } catch (FileNotFoundException ex) {
                ex.printStackTrace ();
            } catch (DocumentException ex) {
                ex.printStackTrace ();
            }
        }}

    );
    popupMenu.add (mntmPrintTaskAssignments);
    JMenuItem mntmPrintTaskAssignments2 = new JMenuItem (""Print All Task Assignment Forms"");
    mntmPrintTaskAssignments2.addActionListener (new ActionListener () {
        public void actionPerformed (ActionEvent e) {
            Document document = new Document ();
            if (""A4"".equals (SMTSingleton.getSingletonInstance ().getProperties ().getProperties ().get (SMTProperties.KEY_PAPERSIZE))) {
                document.setPageSize (PageSize.A4);
            } else {
                document.setPageSize (PageSize.LETTER);
            }
            try {
                String filename = ""TaskList_ICS-204_with_Appendixes.pdf"";
                PdfWriter.getInstance (document, new FileOutputStream (filename));
                document.open ();
                TaskList tasks = ((TaskList) table.getModel ());
                tasks.writeToPdf (document);
                for (int i = 0;
                i < tasks.getRowCount (); i ++) {
                    tasks.getTaskAt (i).writeToPdf (document);
                }
                document.close ();
            } catch (FileNotFoundException ex) {
                ex.printStackTrace ();
            } catch (DocumentException ex) {
                ex.printStackTrace ();
            }
        }}

    );
    JMenuBar menuBar = new JMenuBar ();
    add (menuBar, BorderLayout.NORTH);
    menuBar.add (getTaskCreationMenu ());
    menuBar.add (mntmPrintTaskAssignments2);
}
",2111179,"public static void main (String [] args) {
    Document document = new Document ();
    try {
        PdfWriter writer = PdfWriter.getInstance (document, new FileOutputStream (""results/in_action/chapterX/tooltip3.pdf""));
        document.open ();
        writer.setPageEvent (new TooltipExample3 ());
        Paragraph p = new Paragraph (""Hello World "");
        Chunk c = new Chunk (""tooltip"");
        c.setGenericTag (""This is my tooltip."");
        p.add (c);
        document.add (p);
    } catch (DocumentException de) {
        System.err.println (de.getMessage ());
    } catch (IOException ioe) {
        System.err.println (ioe.getMessage ());
    }
    document.close ();
}
",Write PDF File,Type-3 (WT3/4),FALSE
2016059,"private void ZipCode (NpsContext ctxt, ZipOutputStream out) throws Exception {
    String filename = ""JOB"" + GetId () + "".data"";
    out.putNextEntry (new ZipEntry (filename));
    try {
        ZipWriter writer = new ZipWriter (out);
        writer.print (code);
    } finally {
        out.closeEntry ();
    }
}
",15375411,"public synchronized void backupStore (String name) throws IOException {
    if (null != name && name.length () > 0) {
        String path = this.directoryPath + File.separator + name;
        File file = new File (path);
        if (file.exists () && file.isDirectory ()) {
            String list [] = file.list ();
            byte [] buf = new byte [1024];
            ZipOutputStream out = null;
            String zipFileName = null;
            try {
                zipFileName = this.directoryPath + File.separator + ""backup_"" + System.currentTimeMillis () + ""_"" + name + "".zip"";
                out = new ZipOutputStream (new FileOutputStream (zipFileName));
            } catch (FileNotFoundException x) {
                getLogger ().error (""This should never happen"", x);
                throw new IOException (""Couldn't get ZipFile ("" + zipFileName + "")!"");
            }
            for (int i = 0;
            i < list.length; i ++) {
                try {
                    FileInputStream in = new FileInputStream (path + File.separator + list [i]);
                    out.putNextEntry (new ZipEntry (list [i]));
                    int len;
                    while ((len = in.read (buf)) > 0) {
                        out.write (buf, 0, len);
                    }
                    out.closeEntry ();
                    in.close ();
                } catch (IOException x) {
                    getLogger ().error (x.getMessage (), x);
                }
            }
            out.close ();
        } else {
            throw new IOException (""Invalid Store ("" + name + "")!"");
        }
    } else {
        throw new IOException (""Invalid Store ("" + name + "")!"");
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
2014383,"public static void copyFile (String source, String destination, TimeSlotTracker timeSlotTracker) {
    LOG.info (""copying ["" + source + ""] to ["" + destination + ""]"");
    BufferedInputStream sourceStream = null;
    BufferedOutputStream destStream = null;
    try {
        File destinationFile = new File (destination);
        if (destinationFile.exists ()) {
            destinationFile.delete ();
        }
        sourceStream = new BufferedInputStream (new FileInputStream (source));
        destStream = new BufferedOutputStream (new FileOutputStream (destinationFile));
        int readByte;
        while ((readByte = sourceStream.read ()) > 0) {
            destStream.write (readByte);
        }
        Object [] arg = {destinationFile.getName ()};
        String msg = timeSlotTracker.getString (""datasource.xml.copyFile.copied"", arg);
        LOG.fine (msg);
    } catch (Exception e) {
        Object [] expArgs = {e.getMessage ()};
        String expMsg = timeSlotTracker.getString (""datasource.xml.copyFile.exception"", expArgs);
        timeSlotTracker.errorLog (expMsg);
        timeSlotTracker.errorLog (e);
    } finally {
        try {
            if (destStream != null) {
                destStream.close ();
            }
            if (sourceStream != null) {
                sourceStream.close ();
            }
        } catch (Exception e) {
            Object [] expArgs = {e.getMessage ()};
            String expMsg = timeSlotTracker.getString (""datasource.xml.copyFile.exception"", expArgs);
            timeSlotTracker.errorLog (expMsg);
            timeSlotTracker.errorLog (e);
        }
    }
}
",9746855,"public static boolean copy (InputStream is, File file) {
    try {
        FileOutputStream fos = new FileOutputStream (file);
        IOUtils.copy (is, fos);
        is.close ();
        fos.close ();
        return true;
    } catch (Exception e) {
        System.err.println (e.getMessage ());
        return false;
    }
}
",Copy File,Type-3 (WT3/4),TRUE
742784,"public boolean create () {
    DirectoryManager d = new DirectoryManager (dirSource);
    Vector < String > filenames = new Vector < String > ();
    d.getAllMyFileNames (filenames, true, false);
    byte [] buf = new byte [1024];
    try {
        ZipOutputStream out = null;
        BufferedOutputStream outStream = null;
        SevenZip.Compression.LZMA.Encoder encoder = null;
        boolean eos = false;
        if (! useLZMA) {
            out = new ZipOutputStream (new FileOutputStream (zip));
        } else {
            outStream = new BufferedOutputStream (new FileOutputStream (new File (zip)));
            encoder = new SevenZip.Compression.LZMA.Encoder ();
            encoder.SetAlgorithm (2);
            encoder.SetDictionarySize (1 << 21);
            encoder.SeNumFastBytes (128);
            encoder.SetMatchFinder (1);
            encoder.SetLcLpPb (3, 0, 2);
            encoder.SetEndMarkerMode (eos);
            encoder.WriteCoderProperties (outStream);
        }
        for (int i = 0;
        i < filenames.size (); i ++) {
            myMaster.writeOnLog (""processing : "" + filenames.elementAt (i) + "" to create "" + filenames.elementAt (i).replace (d.getDirectory (), """"));
            if (! useLZMA) {
                FileInputStream in = new FileInputStream (filenames.elementAt (i));
                out.putNextEntry (new ZipEntry (filenames.elementAt (i).replace (d.getDirectory (), """")));
                int len;
                while ((len = in.read (buf)) > 0) {
                    out.write (buf, 0, len);
                }
                out.closeEntry ();
                in.close ();
            } else {
                File inFile = new File (filenames.elementAt (i));
                BufferedInputStream inStream = new BufferedInputStream (new FileInputStream (new File (filenames.elementAt (i))));
                long fileSize;
                if (eos) fileSize = - 1;
                else fileSize = inFile.length ();

                for (int j = 0;
                j < 8; j ++) outStream.write ((int) (fileSize>>> (8 * j)) & 0xFF);

                encoder.Code (inStream, outStream, - 1, - 1, null);
                inStream.close ();
            }
            myMaster.setProgress (1);
        }
        if (! useLZMA) out.close ();
        else {
            outStream.flush ();
            outStream.close ();
        }
    } catch (IOException e) {
        myMaster.writeOnLog (""error while creating zip file : "" + e);
        return false;
    }
    return true;
}
",6418269,"protected void packRec (File file, ZipOutputStream zos) throws IOException {
    if (file.isDirectory ()) {
        String [] children = file.list ();
        for (int i = 0;
        i < children.length; i ++) {
            packRec (new File (file, children [i]), zos);
        }
    } else {
        String filePath = file.getPath ();
        String entryPath = filePath.substring (dir.length () + 1).replace ('\\', '/');
        ZipEntry entry = new ZipEntry (entryPath);
        zos.putNextEntry (entry);
        FileInputStream fis = new FileInputStream (file);
        byte [] b = new byte [2048];
        int tmpLen;
        while ((tmpLen = fis.read (b)) != - 1) {
            zos.write (b, 0, tmpLen);
        }
        zos.flush ();
        fis.close ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
13210305,"public static final String encryptMD5 (String decrypted) {
    try {
        MessageDigest md5 = MessageDigest.getInstance (""MD5"");
        md5.update (decrypted.getBytes ());
        byte hash [] = md5.digest ();
        md5.reset ();
        return hashToHex (hash);
    } catch (NoSuchAlgorithmException _ex) {
        return null;
    }
}
",19178250,"public static String createMD5 (String str) {
    String sig = null;
    String strSalt = str + sSalt;
    try {
        MessageDigest md5 = MessageDigest.getInstance (""MD5"");
        md5.update (strSalt.getBytes (), 0, strSalt.length ());
        byte byteData [] = md5.digest ();
        StringBuffer sb = new StringBuffer ();
        for (int i = 0;
        i < byteData.length; i ++) {
            sb.append (Integer.toString ((byteData [i] & 0xff) + 0x100, 16).substring (1));
        }
        sig = sb.toString ();
    } catch (NoSuchAlgorithmException e) {
        System.err.println (""Can not use md5 algorithm"");
    }
    return sig;
}
",Secure Hash,Type-3 (WT3/4),TRUE
6856298,"public static void copyFile (File from, File to) throws IOException {
    ensureFile (to);
    FileChannel srcChannel = new FileInputStream (from).getChannel ();
    FileChannel dstChannel = new FileOutputStream (to).getChannel ();
    dstChannel.transferFrom (srcChannel, 0, srcChannel.size ());
    srcChannel.close ();
    dstChannel.close ();
}
",20508693,"private void zip (FileHolder fileHolder, int zipCompressionLevel) {
    byte [] buffer = new byte [BUFFER_SIZE];
    int bytes_read;
    if (fileHolder.selectedFileList.size () == 0) {
        return;
    }
    File zipDestFile = new File (fileHolder.destFiles [0]);
    try {
        ZipOutputStream outStream = new ZipOutputStream (new FileOutputStream (zipDestFile));
        for (int i = 0;
        i < fileHolder.selectedFileList.size (); i ++) {
            File selectedFile = fileHolder.selectedFileList.get (i);
            super.currentObjBeingProcessed = selectedFile;
            this.inStream = new FileInputStream (selectedFile);
            ZipEntry entry = new ZipEntry (selectedFile.getName ());
            outStream.setLevel (zipCompressionLevel);
            outStream.putNextEntry (entry);
            while ((bytes_read = this.inStream.read (buffer)) != - 1) {
                outStream.write (buffer, 0, bytes_read);
            }
            outStream.closeEntry ();
            this.inStream.close ();
        }
        outStream.close ();
    } catch (IOException e) {
        errEntry.setThrowable (e);
        errEntry.setAppContext (""gzip()"");
        errEntry.setAppMessage (""Error zipping: "" + zipDestFile);
        logger.logError (errEntry);
    }
    return;
}
",Copy File,Type-3 (WT3/4),TRUE
10673772,"private File extractResource (String resourceName, File destDir) {
    File file = new File (destDir, resourceName);
    InputStream in = getClass ().getResourceAsStream (resourceName);
    try {
        FileOutputStream out = FileUtils.openOutputStream (file);
        try {
            IOUtils.copy (in, out);
        } finally {
            if (out != null) {
                out.close ();
            }
        }
    } finally {
        if (in != null) {
            in.close ();
        }
    }
    return file;
}
",11499032,"private void outputSignedOpenDocument (byte [] signatureData) throws IOException {
    LOG.debug (""output signed open document"");
    OutputStream signedOdfOutputStream = getSignedOpenDocumentOutputStream ();
    if (null == signedOdfOutputStream) {
        throw new NullPointerException (""signedOpenDocumentOutputStream is null"");
    }
    ZipOutputStream zipOutputStream = new ZipOutputStream (signedOdfOutputStream);
    ZipInputStream zipInputStream = new ZipInputStream (this.getOpenDocumentURL ().openStream ());
    ZipEntry zipEntry;
    while (null != (zipEntry = zipInputStream.getNextEntry ())) {
        if (! zipEntry.getName ().equals (ODFUtil.SIGNATURE_FILE)) {
            zipOutputStream.putNextEntry (zipEntry);
            IOUtils.copy (zipInputStream, zipOutputStream);
        }
    }
    zipInputStream.close ();
    zipEntry = new ZipEntry (ODFUtil.SIGNATURE_FILE);
    zipOutputStream.putNextEntry (zipEntry);
    IOUtils.write (signatureData, zipOutputStream);
    zipOutputStream.close ();
}
",Copy File,Type-3 (WT3/4),TRUE
1579007,"private void nextZipEntry (String url, int level) throws IOException {
    if (! url.startsWith (""META-INF/"") && ! url.startsWith (""OEBPS/"")) url = ""OEBPS/"" + url;

    ZipEntry ze = new ZipEntry (url);
    ze.setMethod (ZipEntry.DEFLATED);
    tmpzos.putNextEntry (ze);
}
",10041940,"public void zipFile (FileEntry fileEntry) {
    String zipfilename = fileEntry.getPath ();
    if (fileEntry.isDir ()) {
        zipfilename += "".zip"";
    } else {
        zipfilename = zipfilename.substring (0, zipfilename.length () - 4) + "".zip"";
    }
    try {
        ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (new FileOutputStream (zipfilename)));
        out.setLevel (Deflater.DEFAULT_COMPRESSION);
        byte [] data = new byte [1000];
        BufferedInputStream in = new BufferedInputStream (new FileInputStream (fileEntry.getPath ()));
        int count;
        out.putNextEntry (new ZipEntry (fileEntry.getName ()));
        while ((count = in.read (data, 0, 1000)) != - 1) {
            out.write (data, 0, count);
        }
        in.close ();
        out.flush ();
        out.close ();
    } catch (Exception e) {
        e.printStackTrace ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
427727,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",13901736,"public void archive (String [] fileNames, String archiveName) {
    byte [] buffer = new byte [1024];
    try {
        ZipOutputStream zipOut = new ZipOutputStream (new FileOutputStream (archiveName));
        for (int i = 0;
        i < fileNames.length; i ++) {
            FileInputStream fileIn = new FileInputStream (fileNames [i]);
            zipOut.putNextEntry (new ZipEntry (fileNames [i].replace ('\\', '/')));
            int length;
            while ((length = fileIn.read (buffer)) > 0) {
                zipOut.write (buffer, 0, length);
            }
            zipOut.closeEntry ();
            fileIn.close ();
        }
        zipOut.close ();
    } catch (IOException e) {
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
778875,"public BufferedWriter createOutputStream (String inFile, String outFile) throws IOException {
    int k_blockSize = 1024;
    int byteCount;
    char [] buf = new char [k_blockSize];
    File ofp = new File (outFile);
    ZipOutputStream zos = new ZipOutputStream (new FileOutputStream (ofp));
    zos.setMethod (ZipOutputStream.DEFLATED);
    OutputStreamWriter osw = new OutputStreamWriter (zos, ""ISO-8859-1"");
    BufferedWriter bw = new BufferedWriter (osw);
    ZipEntry zot = null;
    File ifp = new File (inFile);
    ZipInputStream zis = new ZipInputStream (new FileInputStream (ifp));
    InputStreamReader isr = new InputStreamReader (zis, ""ISO-8859-1"");
    BufferedReader br = new BufferedReader (isr);
    ZipEntry zit = null;
    while ((zit = zis.getNextEntry ()) != null) {
        if (zit.getName ().equals (""content.xml"")) {
            continue;
        }
        zot = new ZipEntry (zit.getName ());
        zos.putNextEntry (zot);
        while ((byteCount = br.read (buf, 0, k_blockSize)) >= 0) bw.write (buf, 0, byteCount);

        bw.flush ();
        zos.closeEntry ();
    }
    zos.putNextEntry (new ZipEntry (""content.xml""));
    bw.flush ();
    osw = new OutputStreamWriter (zos, ""UTF8"");
    bw = new BufferedWriter (osw);
    return bw;
}
",23247096,"void copyResourceToZip (String entryName, InputStream is, ZipOutputStream zos) throws Exception {
    ZipEntry entry = new ZipEntry (entryName);
    zos.putNextEntry (entry);
    BufferedInputStream bis = new BufferedInputStream (is);
    int avail = bis.available ();
    byte [] buffer = new byte [avail];
    bis.read (buffer, 0, avail);
    zos.write (buffer, 0, avail);
    zos.closeEntry ();
}
",Zip Files,Type-3 (WT3/4),FALSE
1514106,"private void exportLearningUnitView (File selectedFile) {
    if (learningUnitViewElementsManager.isOriginalElementsOnly ()) {
        String [] elementIds = learningUnitViewElementsManager.getAllLearningUnitViewElementIds ();
        for (int i = 0;
        i < elementIds.length; i ++) {
            FSLLearningUnitViewElement element = learningUnitViewElementsManager.getLearningUnitViewElement (elementIds [i], false);
            if (element.getLastModificationDate () == null) {
                element.setLastModificationDate (String.valueOf (new Date ().getTime ()));
                element.setModified (true);
            }
        }
        learningUnitViewElementsManager.setModified (true);
        learningUnitViewManager.saveLearningUnitViewData ();
        if (selectedFile != null) {
            try {
                File outputFile = selectedFile;
                String fileName = outputFile.getName ();
                StringBuffer extension = new StringBuffer ();
                if (fileName.length () >= 5) {
                    for (int i = 5;
                    i > 0; i --) {
                        extension.append (fileName.charAt (fileName.length () - i));
                    }
                }
                if (! extension.toString ().equals ("".fslv"")) {
                    outputFile.renameTo (new File (outputFile.getAbsolutePath () + "".fslv""));
                    outputFile = new File (outputFile.getAbsolutePath () + "".fslv"");
                }
                File files [] = selectedFile.getParentFile ().listFiles ();
                int returnValue = FLGOptionPane.OK_OPTION;
                for (int i = 0;
                i < files.length; i ++) {
                    if (outputFile.getAbsolutePath ().equals (files [i].getAbsolutePath ())) {
                        returnValue = FLGOptionPane.showConfirmDialog (internationalization.getString (""dialog.exportLearningUnitView.fileExits.message""), internationalization.getString (""dialog.exportLearningUnitView.fileExits.title""), FLGOptionPane.OK_CANCEL_OPTION, FLGOptionPane.QUESTION_MESSAGE);
                        break;
                    }
                }
                if (returnValue == FLGOptionPane.OK_OPTION) {
                    FileOutputStream os = new FileOutputStream (outputFile);
                    ZipOutputStream zipOutputStream = new ZipOutputStream (os);
                    ZipEntry zipEntry = new ZipEntry (""dummy"");
                    zipOutputStream.putNextEntry (zipEntry);
                    zipOutputStream.closeEntry ();
                    zipOutputStream.flush ();
                    zipOutputStream.finish ();
                    zipOutputStream.close ();
                    final File outFile = outputFile;
                    (new Thread () {
                        public void run () {
                            try {
                                ZipOutputStream zipOutputStream = new ZipOutputStream (new FileOutputStream (outFile));
                                File [] files = (new File (learningUnitViewManager.getLearningUnitViewOriginalDataDirectory ().getPath ())).listFiles ();
                                int maxSteps = files.length;
                                int step = 1;
                                exportProgressDialog = new FLGImageProgressDialog (null, 0, maxSteps, 0, getClass ().getClassLoader ().getResource (""freestyleLearning/homeCore/images/fsl.gif""), (Color) UIManager.get (""FSLColorBlue""), (Color) UIManager.get (""FSLColorRed""), internationalization.getString (""learningUnitViewExport.rogressbarText""));
                                exportProgressDialog.setCursor (new Cursor (Cursor.WAIT_CURSOR));
                                exportProgressDialog.setBarValue (step);
                                buildExportZipFile ("""", zipOutputStream, files, step);
                                zipOutputStream.flush ();
                                zipOutputStream.finish ();
                                zipOutputStream.close ();
                                exportProgressDialog.setBarValue (maxSteps);
                                exportProgressDialog.setCursor (new Cursor (Cursor.DEFAULT_CURSOR));
                                exportProgressDialog.dispose ();
                            } catch (Exception e) {
                                e.printStackTrace ();
                            }
                        }}

                    ).start ();
                    os.close ();
                }
            } catch (Exception exp) {
                exp.printStackTrace ();
            }
        }
    } else {
    }
}
",20482640,"private void performFileStream (StreamService streamService, final StreamSession session, SubMonitor subMonitor, int numberOfFilesToSend) throws SarosCancellationException {
    OutputStream output = session.getOutputStream (0);
    ZipOutputStream zout = new ZipOutputStream (output);
    int worked = 0;
    int lastWorked = 0;
    int filesSent = 0;
    double increment = 0.0;
    if (numberOfFilesToSend >= 1) {
        increment = (double) 100 / numberOfFilesToSend;
        subMonitor.beginTask (""Streaming files..."", 100);
    } else {
        subMonitor.worked (100);
    }
    try {
        for (String projectID : this.projectFilesToSend.keySet ()) {
            List < IPath > toSend = this.projectFilesToSend.get (projectID);
            zout = new ZipOutputStream (output);
            for (IPath path : toSend) {
                IFile file = sarosSession.getProject (projectID).getFile (path);
                String absPath = file.getLocation ().toPortableString ();
                byte [] buffer = new byte [streamService.getChunkSize () [0]];
                InputStream input = new FileInputStream (absPath);
                ZipEntry ze = new ZipEntry (path.toPortableString ());
                ze.setExtra (projectID.getBytes ());
                zout.putNextEntry (ze);
                int numRead = 0;
                while ((numRead = input.read (buffer)) > 0) {
                    zout.write (buffer, 0, numRead);
                }
                input.close ();
                zout.flush ();
                zout.closeEntry ();
                worked = (int) Math.round (increment * filesSent);
                if ((worked - lastWorked) > 0) {
                    subMonitor.worked ((worked - lastWorked));
                    lastWorked = worked;
                }
                filesSent ++;
                checkCancellation (CancelOption.NOTIFY_PEER);
            }
        }
    } catch (IOException e) {
        error = true;
        log.error (""Error while sending file: "", e);
        localCancel (""An I/O problem occurred while the project's files were being sent: \"""" + e.getMessage () + ""\"" The invitation was cancelled."", CancelOption.NOTIFY_PEER);
        executeCancellation ();
    } catch (SarosCancellationException e) {
        log.debug (""Invitation process was cancelled."");
    } catch (Exception e) {
        log.error (""Unknown exception: "", e);
    } finally {
        try {
            if (filesSent >= 1) zout.finish ();

        } catch (IOException e) {
            log.warn (""IOException occurred when finishing the ZipOutputStream."");
        }
        IOUtils.closeQuietly (output);
        IOUtils.closeQuietly (zout);
    }
    subMonitor.done ();
}
",Zip Files,Type-3 (WT3/4),FALSE
106523,"private void saveZipEntries (Object [] entries, ZipOutputStream zos) throws IOException {
    for (int i = 0;
    i < entries.length;) {
        String entryName = (String) entries [i ++];
        Object entry = entries [i ++];
        zos.putNextEntry (new ZipEntry (entryName));
        if (entry instanceof String) {
            this.saveContents ((String) entry, zos);
        } else {
            this.saveZipEntries ((Object []) entry, zos);
        }
    }
}
",10378347,"private List < ? extends Attachment > createZipAttachment (List < FileSystemItem > nodes, boolean withFolders) throws IOException {
    File tmp = File.createTempFile (""securus"", null);
    ZipOutputStream zip = new ZipOutputStream (new FileOutputStream (tmp));
    try {
        for (FileSystemItem node : nodes) {
            String path;
            if (withFolders) {
                path = node.getFile ();
            } else {
                path = node.getFile ();
            }
            zip.putNextEntry (new ZipEntry (path));
            InputStream in = new BufferedInputStream (node.getContent ());
            int b;
            while ((b = in.read ()) != - 1) {
                zip.write (b);
            }
            zip.closeEntry ();
        }
    } finally {
        zip.close ();
    }
    return Arrays.asList (new ZipAttachment (tmp));
}
",Zip Files,Type-3 (WT3/4),FALSE
5701319,"public static Object [] addObjectToArray (Object [] array, Object obj) {
    Class compType = Object.class;
    if (array != null) {
        compType = array.getClass ().getComponentType ();
    } else if (obj != null) {
        compType = obj.getClass ();
    }

    int newArrLength = (array != null ? array.length + 1 : 1);
    Object [] newArr = (Object []) Array.newInstance (compType, newArrLength);
    if (array != null) {
        System.arraycopy (array, 0, newArr, 0, array.length);
    }
    newArr [newArr.length - 1] = obj;
    return newArr;
}
",14519972,"public static Object resizeArrayIfDifferent (Object source, int newsize) {
    int oldsize = Array.getLength (source);
    if (oldsize == newsize) {
        return source;
    }
    Object newarray = Array.newInstance (source.getClass ().getComponentType (), newsize);
    if (oldsize < newsize) {
        newsize = oldsize;
    }
    System.arraycopy (source, 0, newarray, 0, newsize);
    return newarray;
}
",Resize Array,Type-3 (WT3/4),TRUE
10349782,"public static byte [] encode (String origin, String algorithm) throws NoSuchAlgorithmException {
    String resultStr = null;
    resultStr = new String (origin);
    MessageDigest md = MessageDigest.getInstance (algorithm);
    md.update (resultStr.getBytes ());
    return md.digest ();
}
",23517481,"private String md5 (String uri) throws ConnoteaRuntimeException {
    try {
        MessageDigest messageDigest = MessageDigest.getInstance (""MD5"");
        messageDigest.update (uri.getBytes ());
        byte [] bytes = messageDigest.digest ();
        StringBuffer stringBuffer = new StringBuffer ();
        for (byte b : bytes) {
            String hex = Integer.toHexString (0xff & b);
            if (hex.length () == 1) {
                stringBuffer.append ('0');
            }
            stringBuffer.append (hex);
        }
        return stringBuffer.toString ();
    } catch (NoSuchAlgorithmException e) {
        throw new ConnoteaRuntimeException (e);
    }
}
",Secure Hash,Type-3 (WT3/4),TRUE
1951108,"private void zipStream (InputStream inStream, String streamName, File zipFile) throws IOException {
    if (inStream == null) {
        log.warn (""No stream to zip."");
    } else {
        try {
            FileOutputStream dest = new FileOutputStream (zipFile);
            ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest));
            ZipEntry entry = new ZipEntry (streamName);
            out.putNextEntry (entry);
            copyInputStream (inStream, out);
            out.close ();
            dest.close ();
            inStream.close ();
        } catch (IOException e) {
            log.error (""IOException while zipping stream"");
            throw e;
        }
    }
}
",8504294,"private void storeProcessList (Date date, List < ProcessList > processListes, boolean doNotOverrideFile) {
    final int BUFFER = 2048;
    String filename = BASE_FILES_PATH + serverGroup + ""/processlist/"" + sdf.format (date) + "".zip"";
    if (doNotOverrideFile && new File (filename).exists ()) return;

    try {
        FileOutputStream dest = new FileOutputStream (filename);
        ZipOutputStream out = new ZipOutputStream (new BufferedOutputStream (dest));
        byte data [] = new byte [BUFFER];
        for (ProcessList processList : processListes) {
            ByteArrayInputStream fi = new ByteArrayInputStream (buildProcessListText (processList).getBytes ());
            BufferedInputStream origin = new BufferedInputStream (fi, BUFFER);
            ZipEntry entry = new ZipEntry (processList.getMysqlServer ().getName () + "".txt"");
            out.putNextEntry (entry);
            int count;
            while ((count = origin.read (data, 0, BUFFER)) != - 1) {
                out.write (data, 0, count);
            }
            origin.close ();
        }
        out.close ();
    } catch (Exception e) {
        e.printStackTrace ();
    }
}
",Zip Files,Type-3 (WT3/4),FALSE
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,
,,,,,,