working on validation file parser
new datamodel for parsing of validation reports
new datamodel for parsing of validation reports
updating to version 1.75C
Merge branch 'master' of github.com:andreasprlic/biojava into validation
updating
removing print
 demo of working with large structures
adding demo for cath domains
merging in new code for parsing upcoming wwPDB validation files
Merge branch 'master' of github.com:biojava/biojava
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.