suppose I have a j2ee application running on jBoss or weblogic server, and I have a profiler like jProbe, is it enough or do I have to have a IDE like jdeveloper or eclipse ?
A profiler has nothing to do with IDE. Some IDEs do provide plugins to incorporate profiler features. But that is more of a convenience than a requirement.
Typical profilers like jprobe will require that the profiled application be started from the profiler console. They normally create a custom appserver startup script based on your current script so that it can instrument the application. This also means that most of the profilers are not hot-swappable within a running application. You need to restart the application from the profiler and stop after profiling is done.
There are many opensource profilers also available, which are "minimally" intrusive. Most of them are developed using AOP with runtime weaving of applications. Examples include, cougar, jamon, infrared etc