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The flat file serializing engine is invoked by calling the Serialize method of the IFFDocumentSpec interface. By providing a customized XmlReader as the argument to the method, you can control the final data that gets serialized. Data could be in any format, or could simply be a reader created of off an XmlDocument.
Example
Stream stm = docspec.Serialize(new MyXmlReader(originalXmlReader), Encoding.Unicode);
See Also
Microsoft.BizTalk.Component.Interop.IFFDocumentSpec
Using the Flat File Parsing Engine