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
Fixed several bugs, potentially calling with null argument, and having
array print contents of array instead of address
Fixed bug, class defines clone method but did not implement Cloneable
interface
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