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()
Fixing #202 . Doubles the memory requirement in alignments
Adding test for #202
Better test
Added a quadratic-space global alignment class. Made Alignments.getPairwiseAligner() return the expected global alignment algorithm. Made Alignments methods throw an UnsupportedOperationException instead of returning null.
Added comments to SubstitutionMatrixScorer.
Modifying CrystalTransform toString method
Merge pull request #203 from josemduarte/master

Fixing #202
Making sure that the parent pom sets the jdk version for all children
Another fix for #193
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