Proposal: new menu layout, with examples

James Bonfield jkb at
Mon Apr 30 16:05:40 UTC 2001

On Mon, Apr 30, 2001 at 04:00:32PM +0100, Peter Rice wrote:
> Looks nice - much nicer than the old emboss_menus_orig version!
> Should we have 2 classes of groups in ACD files - one for menus with a
> short name or hierarchy as in this case, and a longer version (called
> 'keywords', perhaps, and derived from the current 'groups') for wossname to
> search?

Thanks for the comments.

That makes sense as we have two specific purposes: wossname and menus.
I like the idea of being able to resort based on expert vs novice. It
shouldn't be too hard to have the choice, but I'm not sure how easy it would
be to do this on-the-fly (at least with my current code).

On the topic of groups - just a warning that we'll also be looking at
restructuring the ACD with the 'group:' type, which is now sounding like a
staggeringly confusing choice of word! By example, take vectorstrip.acd:

group: vecgrp [ info: "Vector sequence" type: frame ]
bool: vectorfile [
        param: Y
        def: Y
        prompt: "Are your vector sequences in a file?"

infile: vectors [
        param: Y
        req: @($(vectorfile)?1:0)
        nullok: Y
        def: ""
        prompt: "Name of vectorfile"

string: linkerA [
        req: @(!$(vectorfile))
        prompt:"5' sequence"

string: linkerB [
        req: @(!$(vectorfile))
        prompt: "3' sequence"
endgroup: vecgrp

In the GUI dialogue this comes out as a labelled frame. We also have the
choice of "type: page" to use tabs in a tabbed notebook. This basically allows 
grouping of command line options into common areas and hence guides the user
through filling out the various dialogues. (Although mostly the defaults will

This is a large amount of work though so we haven't yet started this, except
where absolutely necessary due to the size of the dialogues (showseq).


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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