Compiler for JASM

// sorry for the improper indenting, i copied this from my source

    private void write(String file, char[] Data) throws FileNotFoundException {
        String filename = file;

        FileOutputStream fos = null;
        DataOutputStream dos = null;

        try {

            fos = new FileOutputStream(filename);

            dos = new DataOutputStream(fos);

            for(char d : Data) {
                dos.writeChar(d);
            }

        }
        catch (FileNotFoundException fnfe) {
            System.out.println("File not found" + fnfe);
        }
        catch (IOException ioe) {
            System.out.println("Error while writing to file" + ioe);
        }
        finally {
            try {
                if (dos != null) {
                    dos.close();
                }
                if (fos != null) {
                    fos.close();
                }
            }
            catch (Exception e) {
                System.out.println("Error while closing streams" + e);
            }
        }
    }

    private int get_lines(String file) throws IOException {

        InputStream is = new BufferedInputStream(new FileInputStream(file));
        try {
            byte[] c = new byte[1024];
            int count = 0;
            int readChars = 0;
            boolean empty = true;
            while ((readChars = is.read(c)) != -1) {
                empty = false;
                for (int i = 0; i < readChars; ++i) {
                    if (c[0] == ';') {
                        --count;
                    }
                    if (c[i] == '\n') {
                        ++count;
                    }
                }
            }
            return (count == 0 && !empty) ? 1 : count;
        } finally {
            is.close();
        }
    }

    private static String getChecksum(Serializable object) throws IOException, NoSuchAlgorithmException {
        ByteArrayOutputStream baos = null;
        ObjectOutputStream oos = null;
        try {
            baos = new ByteArrayOutputStream();
            oos = new ObjectOutputStream(baos);
            oos.writeObject(object);
            MessageDigest md = MessageDigest.getInstance("MD5");
            byte[] thedigest = md.digest(baos.toByteArray());
            return DatatypeConverter.printHexBinary(thedigest);
        } finally {
            oos.close();
            baos.close();
        }
    }

    /**
     * Compiles JCPU compatible code.
     * @param file File to compile.
     * @throws FileNotFoundException Thrown when the file doesnt exist.
     */
    public void compile(String file, String toFile) throws FileNotFoundException {
        try {
            String argchk = "NO CHECKSUM DEFINED";
            char[] data = new char[get_lines(file) + 1];
            System.out.println("Compiling " + file + " with about " + (get_lines(file) + 1) + " lines.");
            BufferedReader reader = new BufferedReader(new FileReader(file));
            String line = reader.readLine();
            int chr = 0;
            while (line != null) {
                if(line.startsWith(";")) {
                    System.out.println("New line");
                }
                if(line.startsWith("P,")) {
                    String arg = line.substring(2);
                    int x = Integer.parseInt(arg);
                    if(x > 999) {
                        x = 0;
                    }
                    data[chr] = (char) (0x4000 + x);
                    System.out.println("Print command. Value: " + Integer.toHexString(0x4000 + x));
                }
                if(line.startsWith("CHK,")) {
                    argchk = line.substring(4);
                    System.out.println("Verifying checksum after compile.");
                }
                if(line.startsWith("A,")) {

                    String arg = line.substring(2);
                    int x = Integer.parseInt(arg);
                    if(x > 999) {
                        x = 0;
                    }
                    data[chr] = (char) (0x1000 + x);
                    System.out.println("Write to register A command. Value: " + Integer.toHexString(0x1000 + x));
                }
                if(line.startsWith("B,")) {

                    String arg = line.substring(2);
                    int x = Integer.parseInt(arg);
                    if(x > 999) {
                        x = 0;
                    }
                    data[chr] = (char) (0x2000 + x);
                    System.out.println("Write to register B command. Value: " + Integer.toHexString(0x2000 + x));
                }
                if(line.startsWith("T,")) {
                    String arg = line.substring(2);
                    int x = Integer.parseInt(arg);
                    if(x > 999) {
                        x = 0;
                    }
                    data[chr] = (char) (0x3000 + x);
                    System.out.println("Write to register Temp command. Value: " + Integer.toHexString(0x3000 + x));
                }
                if(line.startsWith("J,")) {

                    String arg = line.substring(2);
                    int x = Integer.parseInt(arg);
                    if(x > 999) {
                        x = 0;
                    }
                    data[chr] = (char) (0x5000 + x);
                    System.out.println("Jump command. Value: " + Integer.toHexString(0x5000 + x));
                }
                if(line.startsWith("M,")) {
                    String arg = line.substring(2);
                    int x = Integer.parseInt(arg);
                    if(x > 999) {
                        x = 0;
                    }
                    data[chr] = (char) (0x6000 + x);
                    System.out.println("Math command. Value: " + Integer.toHexString(0x6000 + x));
                }
                if(line.startsWith("NON")) {
                    System.out.println("Writing a No Line");
                    data[chr] = (char) (0x00EE);
                }
                if(line.startsWith("LIN")) {
                    System.out.println("Writing an enable line");
                    data[chr] = (char) (0x00ED);
                }
                if(line.startsWith("FJT")) {
                    System.out.println("Writing an jump from location");
                    data[chr] = (char) (0x00EF);
                }
                if(line.startsWith("CHC")) {
                    System.out.println("Checksum verify command");
                    data[chr] = (char) (0x00EC);
                }
                if(line.startsWith("END")) {
                    System.out.println("Writing an end");
                    data[chr] = (char) (0xF000);
                }
                if(line.startsWith("RGAB")) {
                    System.out.println("Getting a compare");
                    data[chr] = (char) (0x00EB);
                }
                if(line.startsWith("SKP")) {
                    System.out.println("Skipping over next instruction");
                    data[chr] = (char) (0x00EA);
                }
                chr = chr + 1;
                line = reader.readLine();
            }