[Biojava-l] BioJava translation

[Pjotr Prins]

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.