Shameless reproduction of content from http://www.heatonresearch.com/articles/22/page2.html for my own reference.

The BinaryFile class can be seen in BinaryFile.java. To use the BinaryFile class, create a RandomAccessFile class to the file that you would like to work with. This file can be opened for read or write access. Then construct a BinaryFile object, passing in your RandomAccessFile object to the constructor. The following two lines prepare to read/write to a file called “test.dat”.

file=new RandomAccessFile("test.dat","rw");
bin=new BinaryFile(file);

Once this is complete, you can call the various methods provided, to access different data types. The methods to access the various data types are prefixed with either read or write and then the type. For example, the method to read a fixed length string is readFixedLengthString. The complete class is shown in Listing 1.

Listing 1: Reading Java Binary Files

import java.io.*;

/**
 * @author Jeff Heaton(<a href="http://www.jeffheaton.com" title="http://www.jeffheaton.com">http://www.jeffheaton.com</a>)
 * @version 1.0
 */
class BinaryFile
{

  /**
   * Use this constant to specify big-endian integers.
   */
  public static final short BIG_ENDIAN = 1;

  /**
   * Use this constant to specify litte-endian constants.
   */
  public static final short LITTLE_ENDIAN = 2;

  /**
   * The underlying file.
   */
  protected RandomAccessFile _file;

  /**
   * Are we in LITTLE_ENDIAN or BIG_ENDIAN mode.
   */
  protected short _endian;

  /**
   * Are we reading signed or unsigned numbers.
   */
  protected boolean _signed;

  /**
   * The constructor.  Use to specify the underlying file.
   *
   * @param f The file to read/write from/to.
   */
  public BinaryFile(RandomAccessFile f)
  {
    _file = f;
    _endian = LITTLE_ENDIAN;
    _signed = false;
  }

  /**
   * Set the endian mode for reading integers.
   *
   * @param i Specify either LITTLE_ENDIAN or BIG_ENDIAN.
   * @exception java.lang.Exception Will be thrown if this method is 
   * not passed either BinaryFile.LITTLE_ENDIAN or BinaryFile.BIG_ENDIAN.
   */
  public void setEndian(short i) throws Exception
  {
    if ((i == BIG_ENDIAN) || (i == LITTLE_ENDIAN))
      _endian = i;
    else
      throw (new Exception(
          "Must be BinaryFile.LITTLE_ENDIAN or BinaryFile.BIG_ENDIAN"));
  }

  /**
   * Returns the endian mode.  Will be either BIG_ENDIAN or LITTLE_ENDIAN.
   *
   * @return BIG_ENDIAN or LITTLE_ENDIAN to specify the current endian mode.
   */
  public int getEndian()
  {
    return _endian;
  }

  /**
   * Sets the signed or unsigned mode for integers.  true for signed, false for unsigned.
   *
   * @param b True if numbers are to be read/written as signed, false if unsigned.
   */
  public void setSigned(boolean b)
  {
    _signed = b;
  }

  /**
   * Returns the signed mode.
   *
   * @return Returns true for signed, false for unsigned.
   */
  public boolean getSigned()
  {
    return _signed;
  }

  /**
   * Reads a fixed length ASCII string.
   *
   * @param length How long of a string to read.
   * @return The number of bytes read.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public String readFixedString(int length) throws java.io.IOException
  {
    String rtn = "";

    for (int i = 0; i &lt; length; i++)
      rtn += (char) _file.readByte();
    return rtn;
  }

  /**
   * Writes a fixed length ASCII string.  Will truncate the string if it does not fit in the specified buffer.
   *
   * @param str The string to be written.
   * @param length The length of the area to write to.  Should be larger than the length of the string being written.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public void writeFixedString(String str, int length)
      throws java.io.IOException
  {
    int i;

    // trim the string back some if needed

    if (str.length() &gt; length)
      str = str.substring(0, length);

    // write the string

    for (i = 0; i &lt; str.length(); i++)
      _file.write(str.charAt(i));

    // buffer extra space if needed

    i = length - str.length();
    while ((i--) &gt; 0)
      _file.write(0);
  }

  /**
   * Reads a string that stores one length byte before the string.  
   * This string can be up to 255 characters long.  Pascal stores strings this way.
   *
   * @return The string that was read.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public String readLengthPrefixString() throws java.io.IOException
  {
    short len = readUnsignedByte();
    return readFixedString(len);
  }

  /**
   * Writes a string that is prefixed by a single byte that specifies the length of the string.  This is how Pascal usually stores strings.
   *
   * @param str The string to be written.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public void writeLengthPrefixString(String str) throws java.io.IOException
  {
    writeByte((byte) str.length());
    for (int i = 0; i &lt; str.length(); i++)
      _file.write(str.charAt(i));
  }

  /**
   * Reads a fixed length string that is zero(NULL) terminated.  This is a type of string used by C/C++.  For example char str[80].
   *
   * @param length The length of the string.

   * @return The string that was read.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public String readFixedZeroString(int length) throws java.io.IOException
  {
    String rtn = readFixedString(length);
    int i = rtn.indexOf(0);
    if (i != -1)
      rtn = rtn.substring(0, i);
    return rtn;
  }

  /**
   * Writes a fixed length string that is zero terminated.  This is the format generally used by C/C++ for string storage.
   *
   * @param str The string to be written.
   * @param length The length of the buffer to receive the string.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public void writeFixedZeroString(String str, int length)
      throws java.io.IOException
  {
    writeFixedString(str, length);
  }

  /**
   * Reads an unlimited length zero(null) terminated string.
   *
   * @return The string that was read.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public String readZeroString() throws java.io.IOException
  {
    String rtn = "";
    char ch;

    do
    {
      ch = (char) _file.read();
      if (ch != 0)
        rtn += ch;
    } while (ch != 0);
    return rtn;
  }

  /**
   * Writes an unlimited zero(NULL) terminated string to the file.
   *
   * @param str The string to be written.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public void writeZeroString(String str) throws java.io.IOException
  {
    for (int i = 0; i &lt; str.length(); i++)
      _file.write(str.charAt(i));
    writeByte((byte) 0);
  }

  /**
   * Internal function used to read an unsigned byte.  External classes should use the readByte function.
   *
   * @return The byte, unsigned, as a short.
   * @exception java.io.IOException If an IO exception occurs.
   */
  protected short readUnsignedByte() throws java.io.IOException
  {
    return (short) (_file.readByte() & 0xff);
  }

  /**
   * Reads an 8-bit byte.  Can be signed or unsigned depending on the signed property.
   *
   * @return A byte stored in a short.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public short readByte() throws java.io.IOException
  {
    if (_signed)
      return (short) _file.readByte();
    else
      return (short) _file.readUnsignedByte();
  }

  /**
   * Writes a single byte to the file.
   *
   * @param b The byte to be written.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public void writeByte(short b) throws java.io.IOException
  {
    _file.write(b & 0xff);
  }

  /**
   * Reads a 16-bit word.  Can be signed or unsigned depending on the signed property.  
   * Can be little or big endian depending on the endian property.
   *
   * @return A word stored in an int.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public int readWord() throws java.io.IOException
  {
    short a, b;
    int result;

    a = readUnsignedByte();
    b = readUnsignedByte();

    if (_endian == BIG_ENDIAN)
      result = ((a &lt;&lt; 8) | b);
    else
      result = (a | (b &lt;&lt; 8));

    if (_signed)
      if ((result & 0x8000) == 0x8000)
        result = -(0x10000 - result);

    return result;
  }

  /**
   * Write a word to the file.
   *
   * @param w The word to be written to the file.
   * @exception java.io.IOException If an IO exception occurs.
   */

  public void writeWord(int w) throws java.io.IOException
  {
    if (_endian == BIG_ENDIAN)
    {
      _file.write((w & 0xff00) &gt;&gt; 8);
      _file.write(w & 0xff);
    } else
    {
      _file.write(w & 0xff);
      _file.write((w & 0xff00) &gt;&gt; 8);
    }
  }

  /**
   * Reads a 32-bit double word.  Can be signed or unsigned 
   * depending on the signed property.  Can be little or big endian depending on the endian property.
   *
   * @return A double world stored in a long.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public long readDWord() throws java.io.IOException
  {
    short a, b, c, d;
    long result;

    a = readUnsignedByte();
    b = readUnsignedByte();
    c = readUnsignedByte();
    d = readUnsignedByte();

    if (_endian == BIG_ENDIAN)
      result = ((a &lt;&lt; 24) | (b &lt;&lt; 16) | (c &lt;&lt; 8) | d);
    else
      result = (a | (b &lt;&lt; 8) | (c &lt;&lt; 16) | (d &lt;&lt; 24));

    if (_signed)
      if ((result & 0x80000000L) == 0x80000000L)
        result = -(0x100000000L - result);

    return result;
  }

  /**
   * Writes a double word to the file.
   *
   * @param d The double word to be written to the file.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public void writeDWord(long d) throws java.io.IOException
  {
    if (_endian == BIG_ENDIAN)
    {
      _file.write((int) (d & 0xff000000) &gt;&gt; 24);
      _file.write((int) (d & 0xff0000) &gt;&gt; 16);
      _file.write((int) (d & 0xff00) &gt;&gt; 8);
      _file.write((int) (d & 0xff));
    } else
    {
      _file.write((int) (d & 0xff));
      _file.write((int) (d & 0xff00) &gt;&gt; 8);
      _file.write((int) (d & 0xff0000) &gt;&gt; 16);
      _file.write((int) (d & 0xff000000) &gt;&gt; 24);
    }
  }

  /**
   * Allows the file to be aligned to a specified byte boundary.  
   * For example, if a 4(double word) is specified, the file pointer will be 
   * moved to the next double word boundary.
   *
   * @param a The byte-boundary to align to.
   * @exception java.io.IOException If an IO exception occurs.
   */
  public void align(int a) throws java.io.IOException
  {
    if ((_file.getFilePointer() % a) &gt; 0)
    {
      long pos = _file.getFilePointer() / a;
      _file.seek((pos + 1) * a);
    }
  }
}