Binary I/O: Changing a String inside a Binary File

Question

Hi people, good morning!
I have written a method here which takes two files as parameters. The method opens the first file (which may or may not be binary) using FileInputStream, loading it into a byte array. This byte array is converted to String by a CharsetDecoder (ISO-8859-1 encoding) and then i use indexOf() on this String to find the initial position of the token i need to find.
Then, i transform the replaced token with getBytes() and insert it in the same position as the index found above, writing everything to the second file parameter as bytes to a FileOutputStream.
The problem is that the destination file, when opened with the associated program (Eg: Oracle Forms Builder for *.fmb files) says the file is corrupt. Seeing that the original file opens and compiles normally, i believe the substitution process is corrupting the file.
Do you know what my code below is missing? Strangely enough, when the replaced token is not larger than the original token, the file is not corrupted...
Any help is greatly appreciated.
Regards!
Thiago Souza
          FileInputStream in = null;
          FileOutputStream out = null;
          try {
               File f = new File(nameFrom);
               in = new FileInputStream(f);
               byte b[] = new byte[(int) f.length()];
               in.read(b);
               Charset cs = Charset.forName("ISO-8859-1");
               CharsetDecoder cd = cs.newDecoder();
               CharsetEncoder ce = cs.newEncoder();
               byte[] headerChange = "$Header: MDBFNDENABLEEVENTS.fmb 115.1 2006/08/10 10:00:00 appldev ship $".getBytes();
            byte[] headerBytes  = "$Header: %f% %v% %d% %u% ship $".getBytes();
               String header       = cd.decode(ByteBuffer.wrap(headerBytes)).toString();
               int headerExcess      = headerChange.length - headerBytes.length;
               header: for (int counter = 0; counter < 30; counter++) {
                    String fileContents = cd.decode(ByteBuffer.wrap(b)).toString();
                    int index = fileContents.indexOf(header);
                    if (index < 0) break header;
                     int headerEnd = index + headerBytes.length;
                     int endChunk = b.length - headerEnd;
                     byte[] initArray  = new byte[index];
                     System.arraycopy(b, 0, initArray, 0, index);
                     byte[] finalArray = new byte[endChunk];
                     System.arraycopy(b, headerEnd, finalArray, 0, endChunk);
                     b = new byte[b.length + headerExcess];
                     System.arraycopy(initArray, 0 , b, 0, index);
                     System.arraycopy(headerChange, 0 , b, index, headerChange.length);
                     System.arraycopy(finalArray, 0, b, headerEnd + headerExcess, endChunk);
               } //Final FOR
               out = new FileOutputStream(new File(nameTo));
               out.write(b);
               out.flush();
           } finally {
                if (out != null) out.close();
                if (in != null) in.close();
           }

Answer 1

If the file is binary, converting it into a String is not a reversible operation and you will definitely get data corruption. You need to work directly in bytes.