Pise/EMBOSS 2.3.1

Peter Rice peter.rice at uk.lionbioscience.com
Wed Apr 24 09:37:09 UTC 2002

David Mathog wrote:
> Back to the subject at hand. (And this is stream of consciousness, so
> please
> bear with me.) I think that maybe for purposes of interface design there
> should be predefined methods to break out (all) the pieces/options of a
> USA.

Discussion transferred to emboss-dev ...

For filename USAs there are already associated qualifiers for most parts.

It looks to me as though you are really asking for associated qualifiers
for all the bits of USAs. If these qualifiers can also appear in listfiles
then they will work there too. GUIs are then free to display whatever they
want, and to pass the bits to EMBOSS to reassemble.

All the qualifiers should start with -s (like -sformat) to keep them

For USAs like genbank:* it gets a little tricky ... that is an EMBOSS
database definition, but maybe the bits of a database definition could be
passed in the USA too (look at emboss.default to see what you would need).
We could allow incomplete database definitions for that, for example by
adding a new database attribute (so showdb can warn about them), or the
command line could override settings in emboss.default.

How the GUI handles all this is of course not an EMBOSS problem :-) I
assume no GUI will want to use all the USA options, but they can make life

GUI developers ... what extra USA associated qualifiers would you like?


Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723

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