Changes to contig editor

James Bonfield jkb at mrc-lmb.cam.ac.uk
Mon Apr 3 12:39:20 EST 2000

Following on from a few comments at a recent course, I am looking at a 
few cosmetic changes to the contig editor. Some (but not all) of these
can easily be made user-configurable, so they shouldn't cause too many
problems. I am posting here in order to obtain user feedback. Please
speak up now, or suffer in silence whatever changes we decide!

1. Consensus at the top. This has the great advantage of allowing
quickly scrolling along without the consensus consistently moving up
and down.

One person suggested that we make the editor window user resizable and 
that it should stay fixed at that size. However I'm unsure of exactly
what this gains (and I think that the request was based more on
annoyance of a continuously moving consensus). Any comments?

2. The status lines, when the consensus is displayed at the top,
should be above the consensus. When the consensus is displayed at the
bottom they'll be below the consensus. This has some vague symmetry,
but realistically it is designed to make sure that the consensus is
close to the sequences.

3. Where do we put the ruler when the consensus is displayed at the
top? I think it looks best between the consensus and individual
sequences. An alternative is between the consensus and status lines,
or finally at the top where it's always been. Unless we take the last
option then this has implications for the names display as the very
top line in the "DNA sequences" window does not have a corresponding
line in the "sequence name" window.

4. In order to cure the problem in (3), we could remove the C: and Q:
values from the main display and put the << < > >> buttons in their
place. (The C: and Q: values would be adjustable from a dialogue
brought up using the settings menu). How often do people adjust these
values during editing? Alternatively we could remove the << < > >>
buttons as they duplicate functionality of the scrollbar, but
personally I prefer having these scroll buttons next to one another
rather than spread out over a large X distance (making fine scroll
movement a laborious mouse-moving task).

Most of these issues are fairly simple to code, but we do not wish to
support all possible combinations. So at present we propose to move
the C: and Q: value boxes into a Settings menu dialogue and put the << 
< > >> buttons in their place. This would be done regardless of where
the consensus is and so would not be user-adjustable. The positioning
of the consensus however will be user adjustable.

Please DO pass your thoughts on to me, whether positive or negative.


PS. None of these changes have been implemented in the 2000.0 release
- the editor is much the same as it's always been.
James Bonfield (jkb at mrc-lmb.cam.ac.uk)   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 http://www.mrc-lmb.cam.ac.uk/pubseq/

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