[Biojava-dev] Alignments.getPairwiseAlignment seems a bit choosy

[Andreas Prlic]

Hi Hannes,

> I recently ran into a bit of an annoyance when using
> Alignments.getPairwiseAlignment with DNASequences
>
> If the DNASequences do not have the same CompoundSet, the alignment
> fails (but silently, which is the annoying part) - you just get 0 as
> Similars or Identicals.

what gap penalties are you using?

I don't have had enough time to look at the
> code in detail, but there should be something done here, at least
> check and throw an exception or something if it can't be made to work
> regardless.

Can you provide an example to reproduce this?


> Does anyone of you use git to work on biojava? When I start to
> contribute, should I use svn or is there a way to submit pull requests
> that will be incorporated into the code? Is the github mirror just a
> one-way mirror or is the connection bidirectional?


Git is currently read-only. You will need to start with a fresh
checkout from SVN using a developer account. I will talk to you off
list how to get such an account.

Andreas



-- 
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Dr. Andreas Prlic
Senior Scientist, RCSB PDB Protein Data Bank
University of California, San Diego
(+1) 858.246.0526
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