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.
Merge pull request #16 from biojava/master

Catch back up with biojava/master
Merge pull request #17 from biojava/master

Catch back up with biojava/master
Merge pull request #91 from emckee2006/master

Remove Compile warning in a case where we are subverting the type system