abiview

[James Bonfield]

On Thu, Jul 12, 2001 at 09:50:01AM +0200, David Bauer wrote:
> we are doing some tests with the MJGeneSys BaseStation.
> This machine creates output files in SCF 3.00 format. The good old ted
> does not understand these tracefiles.

Ted is _OLD_. I'm suprised anyone still uses it.

The "gap4 viewer" (free to everyone, including commercial users) is
distributed on our ftp site (ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/) and also
contains Trev, a modern replacement for ted. We plan to separate this out
sometime soon so that you don't need to obtain lots of other stuff just to get 
trev - we'll just stick Trev up as a separate download.

The main file reading code from Trev (and previously Ted) is called
io_lib. The source is freely available (under something approximately a BSD
licence) on the LMB ftp site too. This supports ABI, ALF, SCF (v2 and v3) as
well as the newer highly compressed formats CTF and ZTR. We have no issues
with the Emboss team making use of this code in abiview. Io_lib, although
mainly a library, also contains some example programs which includes one to
convert between formats and to convert between SCF versions. (It 
doesn't allow writing to ABI or ALF formats; as both are proprietory we do not 
wish to create code to further their use.)

James

-- 
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   Tel: 01223 402499   Fax: 01223 213556
Medical Research Council - Laboratory of Molecular Biology,
Hills Road, Cambridge, CB2 2QH, England.
Also see Staden Package WWW site at http://www.mrc-lmb.cam.ac.uk/pubseq/