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merkerguitars, I cannot be 100% sure, but most places really don't care what you write your code in. The reason they tell you to use program X to write your code is because then if you have a problem the instructor (or TA) only needs to know the one program.. Every other program is use at your own risk.
If they just ask for the *.java files at the end, then it shouldn't make one iota of a difference what program you use. Heck, you could use a plain text editor (pico, nano, notepad, etc) and write everything that way.
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