required vs optional

[Peter Rice]

James Bonfield wrote:
> But I've already found one case (shuffleseq) where it is stated to be "req: N"
> (and defaults to opt:y), in which case I (wrongly) grey it out as it's never
> needed.

I am a little confused there. This definition:

  int: shuffle [ req: N def: 1 info: "Number of shuffles" ]

is opt: N (the default - all these default to false)

EMBOSS will never prompt for it, but you can certainly set it from the command
line, and if you like you can offer it to the user. EMBOSS will accept
anything on the command line (there is no complaint if the user puts something
on the command line that is not wanted). But the assumption for graphical user
interfaces is that only the optional cases are offered.

I guess, being pedantic, it would be reasonable to change shuffle to be "opt:
y" in the acd file, and the same for most other options you might like to turn
on. My suspicion is that only a few keen users are really using the -options
qualifier, but in any case it was aimed as much at the GUI developer as at the
user who didn't want too many prompts.
 
> And of course there are other cases where the existing syntax is sufficient,
> but it's not actually used (eg all those options in pepwheel).

We could clean them up, or we could remove the 'turn off the plot' option :-)

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