required vs optional

Peter Rice Peter.Rice at
Thu Feb 8 12:19:26 UTC 2001

James Bonfield wrote:
> The defaults are both N, so not specifying either req or opt indicates a
> greyed-out option, which cannot be true surely?

If both are N, EMBOSS will not prompt. The application will always receive a
value, and it can always be set through the command line.

> Can you please spell out for me exactly when we can be sure (during
> processing, not just at the time of producing help) when we know a question
> will be ignored (ie changing it's value has no effect)?

You can't be sure - only the application code can tell you that.

But you can be sure that the command line version will process everything in
one pass so all the information is in the ACD file.

> What if both req and opt are used (ignoring any opt:N and req:N settings)?
> embossdata looks to be the only one that uses both (but I didn't also check
> for param). Filename is defined as opt:Y req:$(fetch). I suppose as it's opt:Y
> then it may be useful and so should never be displayed as greyed-out.

Yes. If opt or req are Y you should not grey out.

> (I have been wondering about an "optional" tab so that the option values are
> automatically put into a separate area of the dialogue.)

That is what we rather expected GUI developers to do.

If you feel daring, you could add an advanced tab for the greyed out ones, but
they may be ignored by the application. Our assumption was that anything that
should appear in the GUI would be opt, but there are certainly some options
that have no opt:Y at present. Feel free to suggest cases for promption to

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

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