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

Andrew Perry ajperry at pansapiens.com
Thu Feb 24 23:14:22 GMT 2011


On Thu, Feb 17, 2011 at 9:49 PM, 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.


Ah, I see. I'd have no objections there.

Andrew Perry

Postdoctoral Fellow
Whisstock Lab
Department of Biochemistry and Molecular Biology
Monash University, Clayton Campus, PO Box 13d, VIC, 3800, Australia.
Mobile: +61 409 808 529
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