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

[Hannes Brandstätter-Müller]

Hi there,

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. 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.

Another question:

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?

Hannes