I\'m looking for a tool that will reverse engineer Java into a sequence diagram BUT also provides the ability to filter out calls to certain libraries.
For example,
I believe the perfect tool to solve your problem is Diver: Dynamic Interactive Views For Reverse Engineering. It provides both static and dynamic sequence diagrams and looks to solve all your requirements from your question.
It is a plugin for Eclipse and lets you:
It's on Github and there is also a project web site
Full Disclosure: I am the current project lead for Diver