Merge pull request #198 from sbliven/master

Changing maven package for protein-comparison-tool to shade
Removing warnings
Improving logging & exceptions in JFatCatClient
Removing warnings
More #111
Removing ad-hoc logger verbosity control
Fixing #193
- also some improvement for #191: now a TranslationException will be
thrown when compound not known
- a few improvements for other issues: #111, #155, #185
Merge pull request #199 from josemduarte/master

Exception handling and logging improvements, solves #193
started to work on a parser for Phosphosite data (data under CCBY_NC) http://www.phosphosite.org
upgrading to latest log4j
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
making access method public
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