biojava/biojava — pull request #207 by sbliven (2014-11-19 17:26:41+00:00)
Title: Merge with sbliven

This adds some pom cleanups:
- Use vecmath 1.3.1
- Take JDK version from the parent pom

Also some code changes:
- Improvements to CrystalTransform class & xtal package
- Warnings and logging improvements

Conflicts:
biojava3-alignment/pom.xml
biojava3-core/pom.xml
biojava3-modfinder/pom.xml
biojava3-phylo/pom.xml
biojava3-protein-disorder/pom.xml