biojava/biojava — pull request #211 by sbliven (2014-12-01 12:44:09+00:00)
Title: Improvements to Structure alignment CLIs

This improves the CLIs for structure alignment methods (CeMain, FatCat*, SmithWaterman3d, etc.). The GUI parameters (configured through a ConfigStrucAligParams subclass) are now available through the command line as well. Enums are also allowed as parameters.

Other AbstractUserArgumentParser subclasses downstream of BioJava will need to be updated to work with the new system.