Genetic codes and other repeated ACD lists

Peter Rice pmr at
Fri Apr 8 10:55:02 UTC 2005

Dr J.C. Ison wrote:

> Peter Rice wrote:
>>I have found a way to save writing and maintaining lists like these in ACD files:
>>Using the "knowntype" attribute it is possible to delet the value atttribute,
>>and to define a standard list using a "resource" definition in the
>>emboss.default (or .embossrc) file like this:
> It'd be cleaner, more flexible and and easier to maintain and if not a 
> requirement now probably an increasing one in the future.  I've two progs 
> that would benefit from it now.

Thanks. Domainatrix I assume. Which ones? I will take a look and see how they 
fit in.

> Couldn't the default be specified in the same place / file as the values themselves?
> Presumably the default value would be needed before run-time proper and could
> be retrieved at the same time as the values are.

Good point. I need to think some more about whether a knowntype should have a 
default. Genetics codes are a good example - we use a default of 0 but 
strictly genetic code numbers are 1 to 23 (0 is code 1 with only ATG as a start).

> I think it would be nice to support both "standard" lists (ie. ones *with* "values" 
> attribute) and the new style.  Perhaps something like:
>       values: "@knowntype"  

A missing value will do this. Normally the value is required, so an ACD 
developer (or parser) will know it needs a value. (I hope :-)

> to indicate to use the knowntype to get the values, *or*
>       values: "0: Standard ... etc" as before.

Yes, that will override the knowntype. Maybe acdvalid can warn if a list or 
select has a knowntype (with its own standadr value) and a defined value attribute

More comments please!


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