[Jalview-discuss] Quick Poll: how do you use the sequence ID/start-end numbering ?

Joel Guenther guenthej at gmail.com
Fri Feb 18 23:49:46 GMT 2011


Jim-

Sorry for the delayed response.

I agree with Andrew that I'd prefer it if Jalview were to accept a
user-defined start position and then calculate what number the last reside
is for the sequence. I was a bit confused by some incorrect end numbers a
while back, and it would be nice to have this bug fixed.

-Joel





On Thu, Feb 17, 2011 at 2:49 AM, Jim Procter
<jprocter at compbio.dundee.ac.uk>wrote:

> Hi Andrew, thanks for responding!
>
> On 17/02/2011 00:12, Andrew Perry wrote:
> > I think in this case the potential for confusion outweighs any utility
> > in being able to restrict the search region for 'Find' by using the
> > user defined start and end positions.
> true, although in fairness - the latter is actually a bug caused by
> Jalview using the end attribute purely for efficiency (to avoid
> searching the tail end of an alignment row for non-gaps after the last
> sequence position had already been reached). What I was actually getting
> at was whether anyone would object to jalview automatically correcting
> the 'end' attribute if it discovers it to be shorter than the number of
> non-gap symbols in the sequence.
>
> > My vote would be to make 'Find' work on the full length sequence and
> > ignore the /1-X numbering.
> That's my preferred solution, in this case and and for any of the other
> cases where the end attribute was being used. It's really only useful
> for visualization, and for (eventually) indicating if a sequence is
> forward or reverse sense.
> > I've noticed that if you select a region within an alignment (ie by
> > dragging the mouse) then 'Find' is restricted to this region - that
> > functionality should be enough in the case where someone wanted to
> > search within a defined region.
> glad you noticed  ;) !
>
> Jim.
>
> --
> -------------------------------------------------------------------
> J. B. Procter  (JALVIEW/ENFIN)  Barton Bioinformatics Research Group
> Phone/Fax:+44(0)1382 388734/345764  http://www.compbio.dundee.ac.uk
> The University of Dundee is a Scottish Registered Charity, No. SC015096.
>
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