Marshalling XML file to Java pojo/domain object?

Without knowing the specifics of your issues...it should be possible, but it sounds like this may be a case where you would want to write a schema, use xjc to generate binding objects, unmarshal to the generated binding objects, and then translate to your domain objects in java (or use the generated objects directly if applicable).

Note: I'm the EclipseLink JAXB (MOXy) lead and a member of the JAXB 2 (JSR-222) expert group.

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