We have at a children hospital in Madrid the 3D coordinates of human articulations in several types of movements, particularly from children with cerebral palsy. We intend to program a simulation system to help doctors and other health prodfessionals, even parents, in clinical decision making. Up to now we haven't come across a satisfactory graphics library to help us show a toy child that moves just like the real impaired child.
Might be worth thinking slightly differently. Why don't you create a series of videos and show them in your java app. There are a number of 3d applications that will allow you to create these videos from your motion captures this might simplify the process considerably.
here's a quick example
http://www.youtube.com/watch?v=5CDd7EkyKVI
maybe you can try to interface with Blender, if you really need to stay in java. There are also other 3d engines like http://jmonkeyengine.org/
I hope I've been useful (not my field)
The API Java 3D and Xith3D. If the simulation has to be more accurate (requiring for instance Open GL), JOGL is a good choice.
Another option would be to use a programmable game engine. I use unity3d that can be programmed in either javascript or c#. it will output executables on Windows,Linux, mac,ios, android or as a web application.
it has a free version as well
http://unity3d.com/
you can also create a model with a software modeling (like Maya) you export your model has a fbx file with the skeleton (u can also export an animation) with the fbx file you can do nearly everything with the model.
http://openendedgroup.com/field/LoadingFBXFiles.html
You can also use kinect to make Motion Capture for a model.
https://github.com/torbensko/Kinect-to-Maya-motion-capture
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