I'm a Computer Science undergraduate writing my thesis which is about analyzing open source bioinformatics projects and extracting standalone modules. I need those projects to be written in Java and preferably be stable or mature. So far I've found a bunch of projects via SourceForge and I was wondering if there are any notable ones that are not hosted there. A different repository that has a bioinformatics category would be helpful too.

Here's a list of the most promising projects I have so far:

 - Jenetics
 - JGap
 - Jmol
 - Juicebox
 - Picard
 - RDP Classifier
 - Shim
 - Tassel
 - The Chemistry Development Kit
 - Toxfree
 - TreeView
 - VarScan


Thanks in advance.
 - [MHAP][1] (part of [Canu][2] long read assembler)  
 - The server part of [QTLNetMiner][3] is written in Java https://github.com/KeywanHP/QTLNetMiner
 - PacBio's SMRT Analysis is partially written in Java, but I don't know whether it fits your requisites, it seems to be open source but I can't find a license
 - [JAligner][4]
 - [Jalview][5]

 [1]: https://github.com/marbl/MHAP
 [2]: https://github.com/marbl/canu/tree/master/src/mhap
 [3]: https://ondex.rothamsted.ac.uk/QTLNetMiner/
 [4]: http://jaligner.sourceforge.net/
 [5]: http://www.jalview.org/