Apart from the obvious observation that if the Java application is important then you are working for an idiot - then you have to start from the beginning like

Apart from the obvious observation that if the Java application is important then you are working for an idiot - then you have to start from the beginning like everyone else and read a good book. You will also need to become familiar with whatever IDE is used (Eclipse perhaps). Take it slow, resist making changes in the early stages and build a scratch test version of the system at the earliest opportunity. This can be your play area until you are confident that you are doing the right thing.