EMBOSS whish list

James Bonfield jkb at mrc-lmb.cam.ac.uk
Wed Aug 15 16:22:44 UTC 2001

On Wed, Aug 15, 2001 at 06:11:41PM +0200, Guy Bottu wrote:
> - for graphic display : an X-Window graphic with "zoom" function, also tektronix 
> emulation in color.

Maybe now is the time for a quick plug (sorry). We've (finally) managed to
make an official release of "spin". This includes a graphical interface to
EMBOSS, including the ability to zoom, scroll and superimpose plots.

Spin is still in its early days as an EMBOSS interface (although it has its
own algorithms too, some of which date back to before the dawn of time).

See http://www.mrc-lmb.cam.ac.uk/pubseq/ for more details.

Alas it doesn't solve your other problems.

I've also heard via the grapevine that another graphical interface to EMBOSS
is in development; using Java. Is there any news on the progress of this?

> e.g.   xxx -datafile
> to make a program display its data file names. The data file name should 
> preferable appear in the ACD file so that the parsers that generate pages for 
> the graphical user interfaces can find it.

This is a good point. We found this horrid to do, especially for the programs
that generate an arbitrary number of output files. Before running the programs
we delete all {progname}.dat[0-9]* files. Then after running we do a filename
'glob' to see which files have been created. This works OK, but can really
catch out the user if they try to have an input file named "syco.dat" (for


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/

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