ProteinSequence was using parentSequence as a DNA Sequence.  However,
the field was parameterized to have the same CompoundSet for both the
sequence and its parent.  Attempt to make this more explicit versus the
mostly silent compile warning which is hiding our breaking the type
system here.
Improving TestAltLocs and fixing issue with SiftsChainToUniprotMapping
- now TestAltLocs will test 3PIU with both pdb and cif parsers, before
it depended whether the AtomCache was initialised to one or the other
type of file so result was a bit unpredictable
- SiftsChainToUniprotMapping was not downloading the sifts file and
simply reading a blank file. This was making the corresponding test fail
if run stand-alone (not if run as part of a full mvn intall, in that
case the file was getting downloaded by a previous test)
Merge pull request #16 from biojava/master

Catch back up with biojava/master
 fixing problem when displaying IDs of different length
slowing down rate of requests to Uniprot server
Merge branch 'master' of github.com:andreasprlic/biojava
resolving merge conflict
merging fix for loading issue from sbliven
resolving #76 fixing problem when parsing altLocs
Merge branch 'testsissue'
now using new rules for forking unit test threads
Update maven-surefire-plugin dependency to version 2.17 and other updates
Merge pull request #104 from heuermh/surefire-2_17

Update maven-surefire-plugin dependency to version 2.17 and other update...
Merge pull request #17 from biojava/master

Catch back up with biojava/master
fixing NPE with TestBonds #103
Merge pull request #91 from emckee2006/master

Remove Compile warning in a case where we are subverting the type system
for the fix for #91 to work I believe we need to be more careful with CompoundSets