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
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
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
AtomImpl (serialized class) has member variable class Bond that is not
serialized. Bond class serialized.
Fixed bug, class that implemented clone method did not implement
Cloneable interface
Fixed bug, instance variable tranformationMap in serialized class
PDBHeader was not serializable
Merge pull request #186 from benjamintboyle/master

Bug fixes, in structure base package
Merge pull request #180 from josemduarte/master

Consolidating PDB_DIR/PDB_CACHE_DIR reading