Refactored ModelTransformationMatrix and renamed to
BiologicalAssemblyTransformation. Fixed various classes to correct
generation of biological assemblies from PDB and mmCIF files.
Merge pull request #65 from pwrose/master

Refactored ModelTransformationMatrix and renamed to
Fixing #50 Error in RemoteScopInstallation

Fixes two bugs in RemoteScopInstallation (#50)
* Wrong Unmarshaller was used in XMLUtil
* The root node threw an Exception. Although not
  technically valid, it is common enough that returning
  null is better.
Removing URL print statements from RemoteScopInstallation
Incrementing junit version

4.11 includes name parameter for @Parameters annotation
Adding LocalScopDatabase interface

It simply flags ScopDatabase implementations as requiring no or minimal
internet access.
Streamlining ScopFactory

* Enforce multiton pattern, storing a default version rather than a
  default ScopDatabase
* use BerkeleyScopDatabase for all new local installations
* Remove version-specific methods
Removing hard-coded Scop version strings
Provide much more extensive tests for ScopDatabase.

Added a new parametric ScopDatabaseTest, which can be extended
for each implementation to provide individual tests.

Many tests are sensitive to SCOP version, and may still need
additional test cases for older versions.
Better testing for BerkeleyScopInstallation

Now runs the ScopDatabaseTest suite

Minor adjustment needed for 1.75B revisions
Fixing RemoteScopInstallation version
Adding RemoteScopInstallationTest

Many tests fail, but hopefully server updates will fix that
Added ScopDatabase node test
Handling empty XML responses in RemoteScopInstallation

Empty responses return null. This is consistent with how
null gets encoded as XML.
Implementing comments for remote SCOP installations

* Add code for serializing comments (for server)
* Request comments from the server (for clients)

This commit should not be merged into BioJava without first updating
source.rcsb.org, which is the default server.
Adding version to RemoteScopInstallation

* Add version= parameter to server URLs
* Add tests for additional versions
Adding setScopVersion() method to ScopDatabase

It was already implemented by most classes.