There may be a problem with your XML or a bug in the parser that is being used by JAXB in your configuration. You could try unmarshalling an instance of XMLStreamReader
to force a different parser to be used.
import java.io.File;
import javax.xml.bind.*;
import javax.xml.stream.*;
import javax.xml.transform.stream.StreamSource;
public class Demo {
public static void main(String[] args) throws Exception {
Demo demo = new Demo();
XMLInputFactory xif = XMLInputFactory.newFactory();
File outputFile = new File("input.xml");
XMLStreamReader xsr = xif.createXMLStreamReader(new StreamSource(outputFile));
BlastOutput blastOutput = demo.unmarshalBlastOutput(xsr);
}
private BlastOutput unmarshalBlastOutput(XMLStreamReader xsr) throws Exception {
JAXBContext jc = JAXBContext.newInstance(BlastOutput.class);
Unmarshaller u = jc.createUnmarshaller();
return (BlastOutput) u.unmarshal(xsr);
}
}