[Biojava-l] losing meta-info after multiple sequence alignment

[Spencer Bliven]

I think that 1-based indexing was chosen because that's what's used in
genome databases like GenBank. Thus gene offsets from outside data sources
can be used directly without subtracting 1. That said, almost every time I
write code using sequences I get off-by-one errors, so I understand your
frustration. We should definitely improve documentation so that every method
that takes 1-based indexes are clearly marked.

-Spencer

On Thu, Oct 6, 2011 at 03:37, Hannes Brandstätter-Müller <
biojava at hannes.oib.com> wrote:

> Thanks, I'll try to add what I find out. It's a wiki after all. I'll
> just ask the mailing list if things are unclear before I add stuff to
> the wiki.
>
> One thing that bugged me just now, and since I can't find documentation on
> it:
>
> Why is a sequence indexed by 1-(n+1) instead of 0-n? That's rather
> un-java-like, especially since you just get an OutOfBoundsException,
> and the range is not specified in the javadoc, or I could not find it
> easily in the complex class hierarchy.
>
> Hannes
>
> 2011/10/6 Scooter Willis <HWillis at scripps.edu>:
> > Hannes
> >
> > As you can tell we need to improve the cookbook examples. Since you are
> > going through that process would welcome any contributions you can make.
> >
> > Thanks
> >
> > Scooter
> >
> > On 10/6/11 4:07 AM, "Hannes Brandstätter-Müller" <biojava at hannes.oib.com
> >
> > wrote:
> >
> >>On Thu, Oct 6, 2011 at 09:32, Hannes Brandstätter-Müller
> >><biojava at hannes.oib.com> wrote:
> >>> Hi again!
> >>> What I ran into now is that most of the meta-information of a Sequence
> >>> seems to get lost during the MSA step.
> >>
> >>Okay, that was something caused by following another cookbook script
> >>(that, unfortunately, has absolutely no docs or comments) - I found
> >>the getOriginalSequence() method, can work with that. Thanks!
> >>
> >>Hannes
> >>
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> >
> >
>
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