[Biojava-l] jni and emboss

[Guoneng Zhong]

Hi,
For those who are familiar with Java's native interface, here's a 
question.  Is it possible to write java programs that harness the power 
of open source, non-java bio programs like Emboss and still be 
relatively cross-platform? (At least on UNIX)  I am looking at emboss 
and am impressed that something so comprehensive and open source 
exists.  Though still a novice to biojava, I think that neither biojava 
nor bioperl has even a fraction of the functionalities of emboss, and I 
doubt that either project was meant to be for sequence analysis (more 
like fetching reports and parsing reports and displaying reports and 
sequences, right?).  I am not sure why java can't be used to do 
intensive algorithm executions (Affymetrix's GeneSpring is in java!), 
but currently sequence analysis tools are in C/C++, so is it possible to 
add more functionalities to java programs by accessing native codes 
(rather than the clumsy system calls)?

Just a thought.
G