>>>>> "Guoneng" == Guoneng Zhong <[EMAIL PROTECTED]> writes:
Guoneng> but currently sequence analysis tools are in C/C++, so is Guoneng> it possible to add more functionalities to java programs by Guoneng> accessing native codes (rather than the clumsy system Guoneng> calls)? bioperl provides full access to EMBOSS already. I'm not sure about biojava. At one stage I quite fancied writing an EMBOSS wrapper using JNI code. EMBOSS commands are defined using an external ACD file, which defines exactly what parameters can be supplied so of course this sort of thing is possible. And indeed there have been several people who have done so. PISE for example generates code out in several languages. Jemboss also is a Java front end to EMBOSS and is worth checking out. I have no idea how it invokes EMBOSS. The issue of system calls versus native calls is I think a red herring though. Ultimately if its under the hood and well encapsulated the system calls are no more and no less messy than JNI. And the performance differences are not likely to be significant anyway, except for some of the more trivial commands. The time spent within EMBOSS is likely to be significant. So the amount of time actually launching commands is less of a worry. Phil _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
