Personally, I would just stick to Eclipse. (Actually, that’s what I do when I work on our Java back-end!)
Particularly if you are used to advanced features.
Eclipse maintains an index of all symbols, so searching and refactoring works seamlessly. It can tell the hierarchy of classes, which line calls a given method, etc. It allows to generate getters and setters quickly, to assign a constructor parameter to a new or an existing field, to assign an expression to a new field or local variable, etc. Moreover, it is able to compile itself, in incremental mode. It can even update a running program you edit while debugging the code…
Not to mention the advanced debugging capabilities, among other things something I miss in JS DevTools: the capability to enter a method without entering each method call in the parameters of the method, ie. if you have
foo(bar(), goo.get()), you can enter in
foo() without entering in
bar() nor in
The list can go on…
Of course, with time and dedication, perhaps Atom might approach these features via lot of plugins, but Eclipse has some years of head start, so it might be pointless to try to catch it.
What I wrote about Eclipse is probably true for other main Java IDEs: NetBeans, IntelliJ IDEA, etc.
Sometime, specialized IDEs are better than multipurpose editors. The reverse is true: I tried to edit JS in Eclipse, and quickly turned to smarter editors (WebStorm, then Brackets, then Atom).