biojava/biojava — pull request #204 by dmyersturnbull (2014-11-10 21:45:00+00:00)
Title: Quadratic-space vs linear-space global alignments

I'm submitting a pull request because this does introduce an interface change. The fact that Alignments.getPairwiseAligner() returns null for GLOBAL_LINEAR_SPACE and a linear-space global alignment for LINEAR_SPACE to me is so unexpected that it's simply a bug that should be fixed. However, this change means that users who were aware of this issue will get quadratic-space alignment when the upgrade to BioJava 4. How many users are likely to be relying on this?