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.
 - [htsjdk][1]
 - [gatk][2]
 - [igv][3]
 - [haploview][4] 

...
**Edit** and [using the seqanswer wiki][5].

 [1]: https://github.com/samtools/htsjdk/
 [2]: https://www.broadinstitute.org/gatk/
 [3]: https://www.broadinstitute.org/igv/
 [4]: https://www.broadinstitute.org/scientific-community/science/programs/medical-and-population-genetics/haploview/haploview
 [5]: http://seqanswers.com/w/index.php?title=Special%3AAsk&q=[[Language%3A%3AJava]]&po=&sort_num=&order_num=ASC&eq=yes&p[format]=broadtable&p[limit]=&p[sort]=&p[offset]=&p[headers]=show&p[mainlabel]=&p[link]=all&p[searchlabel]=&p[intro]=&p[outro]=&p[default]=&p[class]=sortable+wikitable+smwtable&eq=yes