Proposal: new menu layout, with examples

Gary Williams, Tel 01223 494522 gwilliam at
Mon Apr 30 15:19:18 UTC 2001

James Bonfield wrote:
> Now that several interfaces to EMBOSS are arriving I feel that it is important
> to have a well structured menu system (as indicated in my last email).


> I now have a proposed layout, included as an attachment. It may be hard to see
> the problem with the existing setup, so I've produce a tcl/tk to display a
> menu tree and created menu specs for how it is now (1.11.0, so nearly now) and
> my new proposed setup. My new layout still has quite a few questionable
> choices, and perhaps I could duplicate more often (although personally I
> dislike that) and split into more cascading menus. However it's a start[1].
> So if you're interested in developing interfaces to EMBOSS, or you are one of
> the developers, please download the following:
> See the README file for information on how to run the tcl/tk app. It ought to
> work OK even on pretty old tcl/tk installations.

Didn't work for me - I just got the wish window and a '%' prompt.
I looked at your 'emboss_menu*' files though to see what your
reorganisation is like.

Some commments (more minor niggles than anything major):

I like much of the reorganisation. 

Firstly, I am a 'splitter', I like having several paths to a program, so
many of my comments related to terseness have been removed from this
version of this message ;-)

Some things seems to be in the wrong place:

I would like to see a 'codon usage' section with things like 'cusp',
'chips' 'syco' 'cai' in.

'nthseq' - not really an 'edit' program - more a 'database organisation'
'textsearch' - looks wrong in 'Search:Misc', maybe change to
'Search:Text' ?
'complex' is now deleted
'marscan' finds a MAR site, this is not really a property of DNA
composition  - I would like to see a 'Features' menu as well as
'Composition'. 'Features' would hold those programs which
can/should/will write out GFF files. So this should go in 'Features:DNA'
'antigenic' - finds antigenic features so should go in
'emowse' - not really protein composition, nore identification - should
probably go somewhere under 'Search'
'helixturnhelix' - features
'pepnet', 'pepwheel' - more of 'Display' programs than 'Composition'
'garnier', 'tmap' - secondary structure
'notseq' - not a 'Display' program - - more a 'database organisation'
program, like 'nthseq'
'tfm', 'wossname' - I would rather see this under 'Help' than 'lost in

> James
> [1] I should also point out that in "Spin" the menu labels are actually the
> program doc lines with the program command name in brackets (eg "Finds DNA
> inverted repeats (einverted)"). However I haven't addressed the issue of a
> common language style for doc names yet.

I enforce a description that has as many keywords as possible and that
fits on a 80 character line when displayed by 'wossname'.

I also try to enforce capital first letter and no ending full-stop (to
shave off an extra character).

I try to capitalise acronyms and database names.

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at  
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK

More information about the emboss-dev mailing list