Merge pull request #24 from biojava/master

Catch back up with Trunk
Merge pull request #25 from biojava/master

Catch back up with Trunk
Merge pull request #26 from biojava/master

Catch back up with Trunk
Improving and unifying the setting of PDB_DIR and PDB_CACHE_DIR
- also improvements for #111 and #155
- some more work to do to make sure AtomCache and the Readers don't
double read the environment variables/system properties
More consolidation on PDB_DIR/PDB_CACHE_DIR reading
- reduced the number of initialisations in AtomCache and readers
- now all chem comp providers use PDB_CACHE_DIR
- a few #111 and #155 fixes
Redoing exception handling in test by using junit4's "expected" #111
SIFTS dir now also goes to PDB_CACHE_DIR instead of PDB_DIR
Cath files now also go to PDB_CACHE_DIR
Making tests use split dir layout
Enhance UniprotProxySequenceReader to be able to parse Uniprot when XML
record is passed as a string.  This is useful if parsing the a large
subset of Uniprot which has been previously downloaded (the Swiss-Prot
xml.gz file, for example).  Also support extracting Uniprot accessions.
Merge pull request #182 from emckee2006/master

Minor enhancement to UniprotProxyParser
Merge pull request #27 from biojava/master

Catch back up with Trunk
Remove compile warnings
Merge pull request #183 from emckee2006/master

Remove compile warnings
More fixes for PDB_DIR reading, plus some #111 and #155
Another small fix for PDB_DIR
Renaming CACHE_DIR to match its value (PDB_CACHE_DIR)

Also removed duplicate definitions
Removing duplicate PDB_DIR definitions.

Everything should use UserConfiguration.PDB_DIR
Merge pull request #186 from benjamintboyle/master

Bug fixes, in structure base package
Merge pull request #1 from sbliven/pdbdir

Renaming CACHE_DIR to match its value (PDB_CACHE_DIR)