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

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.

Comments are welcome, as well as suggestions for better possible fixes to this issue..;