Removing deprecated classes for biojava 4 release
Removing some more warnings
Merge pull request #210 from josemduarte/master

Removing deprecated classes for biojava 4 release
Adding method in StructureInterface
Added some methods. Fixed some #111 and #155
Implemented Rfree parsing. Some deprecated methods removed
Redoing resolution parsing in PDB and handling better hybrid entries
Converting java.logging to slf4j in structure gui, #155
Fixing tests after resolution parsing rewrite
Adding ability to parse Enums for parameters.
Allow custom parameters in structure alignment CLIs.

The CLIs for most structure alignment algorithms derive from
AbstractUserArgumentParser, but there wasn't a good mechanism to
introduce new arguments, since all parameters are stored into a
bean.

Without refactoring everything, this makes the parameter specification
a bit more consistent. The standard parameters are still stored in
a StartupParameters bean, but this is extended by each class to store
the class-specific parameters. Help strings are taken from a
ConfigStrucAligParams subclass, which was previously only used for the
GUI parameters. So the GUI and CLI parameter lists should now match.

The procedure for adding a new CLI implementation is documented in
AbstractUserArgumentParser.

Methods converted to the new system:
* Ce
* CeCP
* FatCat
* SmithWaterman3D

Other AbstractUserArgumentParser implementations downstream of BioJava
will need to be updated to work with the new system.
Removing CE-specific parameters from the default CLI
Incrementing version numbers for StructureAlignments
Consolidate structure alignment -help handling

printHelp() is now required for all UserArgumentProcessors
(moved from it's previous location in StructureAlignment.)
This allows -h, -help, and -version to be handled consistently
in the argument parser rather than in each aligner.

Also cleaned up some 'throw Exception/catch Exception' uses.

Finally, slightly changed the behavior of boolean arguments. Valid
values are nothing (determine value based on '-no' prefix), t/true,
and f/false. Other options give errors rather than defaulting to
false (the Boolean.parseBoolean() behavior).
Adding runCECP.sh to the protein comparison bundle
Fixing CLI wrapper scripts
Minor test fix to reflect updated version number
Adding return value of 1 for errors
Merge pull request #212 from sbliven/StartupParameters

Improvements to Structure alignment CLIs