Is there a way to call STL libraries from JNI, I believe JNI provides a C like interface for native calls, how do we achieve this for the C++ template libraries?
I know this is possible, although I haven't done it myself. But JNI code can crash the JVM if you are not VERY CAREFUL. Also, JNI code is much more difficult to maintain than Java code. I was on one project where the Java -> JNI -> STL and COM code was thrown away and we replaced it with C# accessing the same STL and COM and a socket. We never looked back.
If you are doing only a small amount of JNI, it may be worth it. If you are creating a large interface via JNI, I strongly recommend instead writing the component that interacts with STL in C# instead of Java, and using a socket to communicate between the C# and Java components. It will be far easier to write, test, and maintain.
I have to ask why you find it necessary to use the STL libraries from Java. Is there something in them that's not provided by Java's own massive set of libraries?
I understand why you'd have to call your own code (and I'm assuming you've profiled the Java code and found it wanting, otherwise your effort is wasted) but you seem to be asking how to call STL stuff directly.
We've often had trouble with JNI and it makes our code less portable, so you have to have a very good reason for wanting to use it in our shop, and you have to prove with hard data, why the Java-supplied stuff is not adequate.
I agree that if you're looking for just the plain STL, you could probably use a Java library instead. However, if you insist on wrapping STL, SWIG provides some STL wrapping in JNI out of the box (see this for the basic mechanism), which should produce relatively stable, tested code.