Removing warnings
Improving logging & exceptions in JFatCatClient
Minor changes to xtal and contacts packages

- Converted all classes to use log4j
- Fixed warnings
Add default parameters for interface definitions
Added defaults to StructureInterfaceList asaCalc
Adding toXYZString method to prettify CrystalTransform output
Merging local changes to master

Minor additions and logging fixes
Adding CrystalCell methods & tests

getCellIndices()
transfToOriginCell()
Modifying CrystalTransform toString method
Removing Java version from modules

This allows easier modification in the top-level pom
Removing empty class
Reverting 8faf1889, which intoduced Java 1.7-specific code
Reverting vecmath to 1.3.1

The older version has several practical advantages:
- The Mac JRE includes an old version of vecmath, so trying to use 1.5.1
  results in subtle runtime errors
- 1.3.1 is available through maven central
Merge 'main/master' with 'sbliven/master'

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
Adding array version of CrystalCell#transfToOriginCell
Merge pull request #207 from sbliven/master

Merge with sbliven