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,
Enterprise architect from Sparx claims to be able to reverse engineer java code including generating sequence diagrams - see this section of the user guide
It looks like it can record a debugging session and then you generate the sequence diagram from that
I've not tried it (though have used EA as a modelling tool) so ymmv!
There is a free 30day evaluation download available
JIVE (www.cse.buffalo.edu/jive) will construct a sequence diagram from the execution of a Java program. It has an Exclusion Filter capability will allow you to exclude objects belonging to designated classes or packages. JIVE can draw sequence diagrams for multi-threaded Java program execution. It also has the ability compact large diagrams in both the horizontal and vertical dimension, under user guidance.
I have a tool that meets your requirements exactly. Check it out
http://sourceforge.net/projects/javacalltracer/
In addition to being a reverse engineering tool for java it is also very lightweight. You can control the what you want to record from your java program.
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
JTracert is now discontinued. In place, they recommend http://www.jsonde.com/
Take a look at http://www.maintainj.com
It don't know, whether it can filter library calls, but it has a reasonable graphical front end and seems to trace even very large applications.