[Biojava-dev] DNASequence and reverse complement

[Scooter Willis]

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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