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Thanks for the link and a book I've added to my favourites on Safari. I need to find out more about SAXSources (I was using a StAXSource as the source object for the transform). However, using the JXSAXTransformerFactory implementation, I still get the same error: XML-22004: (Fatal Error) Error while parsing input XML document (null).
I can find very little literature of any kind on doing a StaX->DOM transformation although I would have thought this would have been common for anybody parsing very large XML documents - DOM would be the preferred parsing method but the document size precludes it. The StAX->DOM transformation resolves the problem by converting sub-trees of the source document to DOM.