I have a closed source Java application for which vendor has provided APIs for customization. As I have no other documents, i rely completely on the API's javadoc.
I want to trace what methods are actually called in different classes for a particular use case. Is there any way to do that with eclipse?
Most profilers (like YourKit and JProfiler) support Eclipse integration.
You need to use eclipse TPTP (http://www.eclipse.org/tptp/)
Personally I would use VisualVM or Netbeans profiler if possible
JadClipse is a plug-in that allows you to decompile classes using jad, decompilation is available at the time of debugging.
There are some limitations, jad doesn't support java-5, and try catch functions don't always align nicely, but it can give you a good idea of whats going on inside.
See this thread too is-jad-the-best-java-decompiler
Java Decompiler has an Eclipse plugin, supporting Java 6, and works pretty well to decompile source and see what's inside the class files while debugging.