Genetic codes and other repeated ACD lists

[Peter Rice]

Tim Carver wrote:

>Peter Rice wrote: 
>>3. anyone parsing the ACD file will wonder where the value has gone - perhaps
>>acdpretty can be made to fill in missing values with an environment variable
>>set. Would that be acceptable to those who need it?
> 
> I guess so. If we just loop over the ACD's after installation and get
> 'acdpretty' to convert them that shouldn't be too bad I would have
> thought... it would only need to be done once.

For list: and selction: the acdpretty output would look normal (the value: "" 
attribute can be filled in with the knowntype value).

For matrix: and matrixf: we can leave everything unchanged (add nothing to the 
ACD file in acdpretty), or we can offer a list of known matrix filenames using 
some new attribute name. This is a little tricky ... for the alignment 
programs, there will be separate lists for nucleotide (only EDNAFULL and 
EDNAMAT) and protein (EBLOSUM* and EPAM*) with the allowed values depending on 
the type of the input sequences. Of course, as matrix input the user can 
choose any other available matrix file if the interface allows.

Any prerefence (or any special requests to help JEMBOSS?)

regards,

Peter