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

Jim Procter jprocter at compbio.dundee.ac.uk
Thu Feb 17 10:49:24 GMT 2011

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  ;) ! 


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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