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answers:

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I'm writing a test engine for a Java application that has some of the code written in C. This application uses JNI to access it's native part.

In the engine I'm writing, I use Fest to control de UI and perform the tests. However, I,m blind when dealing with the part that is written in C. I wonder if I can use JNA or JNI to access the native part of the app. I believe that the fact that the application is already running is huge issue here.

A: 

You can access to a running java application with Monitoring and Management for the Java Platform (and tools like jvisualvm and jconsole), and with JavaTM Platform Debugger Architecture (JPDA)

All that is a little complicated... The most useful is the first.

Istao