Theoretically, yes, you can, of course, do this in .Net applications, and there are Java / .Net transitions.
Typically, however, Java / C # hooks are done through P / Invoke or COM - both are quite cumbersome for this kind of thing, and therefore, in fact, this probably won't work as neatly as you might imagine.
Anyway, if you want it, I would recommend that you write a "script engine" (i.e. a wrapper around the C # compiler) in C #, and then pass this to the Java ground via interops, for example:
public ScriptResult(string Script) {
Then you need to think carefully about how your C # scripts will have access to any Java-land functionality, and I think the best way is to implement a .Net wrapper class that calls Java objects through interops.
Using C # as a scripting language from a .Net application is surprisingly simple - see for more information.
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