I'm currently looking for a Java Mesh Library.
If my understanding is correct, this would be something similar to OpenMesh.
All I've found at moment is JMesh 'A Polygonal Mesh Library in Java' (http://jmesh.origo.ethz.ch/) which is still in development.
Context : turning a very large stl file into a Mesh structure (probably winged- or half-edged, but again I'm not too familiar with this field) in order to perform Mesh simplification operations (edge collapse, etc.).
You might take a look at:
JavaMonkeyEngine: http://www.jmonkeyengine.com
LWJGL: http://www.lwjgl.org
the Java3D API might also have useful information of directions to support for what you need.
The existing tools written in C++ (OpenMesh & OpenFlipper) are very well optimized.
Java alternatives are still in development.
While implementing a basic HalfEdge structure (and basic operations like Edge Collapse) in Java is not hard, handling the persistence of data is harder/slower. I have a proof of concept of a HalfEdge structure built in J2EE with persistence via EJB3/Hibernate but alot of work wood be needed to develop all the features of OpenMesh.
Conclusion: use OpenMesh.