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

[Hannes Brandstätter-Müller]

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
>>
>>_______________________________________________
>>Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
>>http://lists.open-bio.org/mailman/listinfo/biojava-l
>
>