[Biojava-l] feature request Sequence Alignment

Andreas Prlic andreas at sdsc.edu
Tue Jul 21 04:26:40 UTC 2009

Hi Andreas,

I was working with the Sequence Alignment package today. In particular
I would be interested to have an alignment display that looks nice in
Playing around with the code it seems the alignment image generation
is closely tied to the actual alignment implementation. Do you think
it would be possible to change this a bit and provide a way so there
could be multiple ways to print out (display) an alignment?

Ideally the core of an alignment would be just a data-container (a
bean?)  and the alignment calculation would operate on this bean. Then
after the alignment has been calculated other objects could be used to
provide a print out based on the data in the container-bean.

Would that make sense and do you think this would be difficult to implement?

Andreas (the other)

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