Re: BioJava translation
Pjotr Prins <[email protected]>
| Newsgroups | gmane.comp.java.bio.general |
|---|---|
| Message-ID | <[email protected]> |
On Wed, Oct 13, 2010 at 05:25:41PM +0100, Andy Yates wrote: > That's great news and should be even faster once we get rid of the requirement to upper case since you're having to parse the same sequence twice. > > I wonder what the C version does to make itself even faster The EMBOSS implementation is fastest by a mile - takes less than 3 seconds. But the code is, uhm, hard to read. I think table lookups will win in C, whatever you try. But it may be an interesting exercise if we can get close. Note I am perhaps not using the fastest JVM. java version "1.6.0_20" Java(TM) SE Runtime Environment (build 1.6.0_20-b02) Java HotSpot(TM) Server VM (build 16.3-b01, mixed mode) Pj. _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l