Document sciXMLDoc = (Document)ptsx.getSciXML().copy();
PaperToScrapBook.importAnnotations(this, sciXMLDoc);
Document safDoc = InlineToSAF.extractSAFs(sciXMLDoc, ptsx.getSciXML(), name);
ptsx.transformSAFs(safDoc);
Document newPubXMLDoc = SAFToInline.safToInline(safDoc, ptsx.getSourceXML(), false);
return newPubXMLDoc;
}