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,
Heatlamp (http://www.jmolly.com/heatlamp/) was designed for exactly this purpose.
It generates interactive (and printable) diagrams from running Java code. You can specify filters to describe which classes, packages, and methods to trace. You can also search, filter, and collapse invocations after the diagram is rendered to further reduce the sequence diagram.
Disclaimer: I'm the author of Heatlamp.