We would be interested in having Java ports of the following algorithms:

- Blast
- Hmmer3

This software is available for $119 with a 15 day return. http://www.tangiblesoftwaresolutions.com/Product_Details/CPlusPlus_to_Java_Converter_Details.html It won't do perfect code but will get you close.

This is also an interesting approach http://code.google.com/p/cibyl/ where I can't imagine would work in a I/O or computationally intensive application. Converting ASM to Bytecode takes out all the parsing headaches. The JIT should still be able to take over and optimize.

I have used this before and works reasonably well. http://tech.novosoft-us.com/product_c2j.jsp You get a Jar file that maps all the ansi C libraries.