Genetic codes and other repeated ACD lists
pmr at ebi.ac.uk
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
> 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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