More on "optional:N" meanings

James Bonfield jkb at
Wed May 2 11:18:19 UTC 2001

Sorry to bring up this topic again, but I've just been confused by another odd 

In remap the "uppercase" variable (which holds a list of positions) is defined 
to be opt:N (implicitly) and def:"".

In my code this has unfortunate consequences. I have, in an advanced tab, an
entry window for the uppercase variable. It has no value inserted in it as the 
default is "". However the program will not let me proceed without filling out 
that entry as it claims I haven't specified a value for a non-optional

I think this is just another case where I've confused optional with
required. (Specifically the assumption that non-optional implies mandatory :-))

I'll update the code as follows. Any argument listed as opt:N req:N, that does
not have a value will simply be ignored (and not supplied as an argument to
the emboss program). Any argument that is listed as req:Y (regardless of
whether it is opt:N or opt:Y) will follow the current 'is it set?" test.

Please comment if I'm wildly off target, otherwise just ignore these ramblings.


James Bonfield (jkb at   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

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