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Moving from C#.NET into Java should be very simple for you. The languages are more alike then they are different. You biggest challenge will probably be getting out of the .NET conventions (variable names start with uppercase like "RepositoryItem Product") and into the Java equivalents (variable names start with lowercase like "RepositoryItem product"). For Java support, the site http://stackoverflow.com/questions/tagged/java is your friend.
Picking up ATG on your own, however, will be the big task. Get training if you can, and ask lots of questions here.
With patience you can pick ATG fast. As you cannot be expert within a day a week or a month. The people Who are professionals had put their lots of effort to become professionals. It will take time . But at the end of day You will learn. And If your new Place is providing you training then you can pick up very fast.
Hope you leave .net Affection aside and not abuse java when you messed with syntax mistake as you are moving to java :)
Hope it helps :)