I use the Netbeans IDE and it can profile any type of Java project, including webapps. When you have a project setup in Netbeans, you simply click on "Profile" and answer a few simple questions.
It is very simple to create a new project and import the existing code into it.
You can see screenshots of this here: http://profiler.netbeans.org/
You can download Netbeans here: http://www.netbeans.org/
VisualVM may also work for you. Several plugins are also available for him. VisualVM has been shipping from the JDK since the JDK 6 was updated. You can check it here: https://visualvm.dev.java.net/
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