[Biojava-dev] DNASequence and reverse complement

[Hannes Brandstätter-Müller]

Yeah, I get the feeling that the support for proteins is way more fleshed
out than the support for sequencing…

I will try to experiment around with the code and see if I need to "fix"
something in the core too for my use-case.




On Wed, May 1, 2013 at 5:14 PM, Scooter Willis <HWillis at scripps.edu> wrote:

>  The features is designed to be flexible as a place holder based on
> position for other data. So you can optimize based on the data you need to
> store.
>
> Not sure any testing was done on maintaing features when returning
> different views of the sequence without looking at the code. An original
> goal was to maintain that linkage going from chromosome dna rna amino acid
> as an example.
>
>
>
>
>
> -------- Original message --------
> From: Hannes Brandstätter-Müller <biojava at hannes.oib.com>
> Date: 05/01/2013 10:43 AM (GMT-05:00)
> To: biojava-dev <biojava-dev at lists.open-bio.org>
> Subject: [Biojava-dev] DNASequence and reverse complement
>
>
> Hi,
>
> I am a bit unclear about DNASequence and Features in biojava3...
> Say I want to attach meta info to a sequence (like quality scores for
> fastq, or other numbers to single bases, how would be the intended or best
> way be?
> Single features for each base? One Feature holding a list of values?
>
> Following that, what if I need a reverse complement DNASequence from the
> previous sequence, how would I do that? The reverseComplement() "only"
> gives me a SequenceView, and how would I ensure the attached values from
> the Feature stay consistent?
>
> Hannes
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