Java and C might look similar but they are a few light-years away. Most notably Java is an OOP language, C is not. Java makes it hard to screw things up while in C...
In C you must be very very careful. Even at simple things such as reading a line from the Console is pain. e.g. you should not use fgets function since the user can supply null input or gets() is also a dangerous function that can be overflown. Therefore you should use the getline() function but it is not part of the ANSI C only GNU C there is .... complicated even at simple things, and don't get me started on pointers...
You can't just automagically convert C program to Java and expect it to work. You can rewrite the same C program in Java but you should be very careful, it is very easy to make a copy paste error.
I would recommend you, if you have the programm running in C, learn good C programming and just use C to do the job.
On the other hand you can make a GUI or whatever in Java and call C functions from Java via the JNI but that is a bit advanced.
Controlling equipment? Maybe there is a "driver" for Java? I am only a bit familiar with EPICS but I know that you need not program in C, you can get a "driver" that enables you to program in Java (CAJ/JCA) and the driver then takes care of the C part.