Implemented all TopLevel SBOLReader. Still need to update new changes
from the updated UML diagram with orientation, location, and ranges.
Parsing internal NestedDocument still needs to be corrected. Lastly,
instead of looping through all NamedProperty multiple times, call
constructor instead of calling .create()
Merge branch 'sbol2' of https://github.com/SynBioDex/libSBOLj.git into sbol2