I've had a bit of a look at your code in jEdit with the syntax highlighter and indenting, and I can see a bunch of syntax errors and stuff - you really need to get those before you can fix the larger problem.
For loop control instructions need to be separated by semicolons:
and you are going to need to out of your switch statement, for starters.
I'd suggest reading up a lot on basic java (I know it is hard when you have a pressing problem) and figuring out how you can convert binary to hexadecimal and vice versa on paper, with psuedocode or just logic, whatever helps you see what is going on. There is a great <a href="http://www.javaranch.com/style.jsp">style guide</a> on this site too, that helps you read your code a lot easier, and will help both your markers (I assume) and other people here read it too.
I’ve looked at a lot of different solutions, and in my humble opinion Aspose is the way to go. Here’s the link: http://aspose.com