import jalview.xml.binding.embl.EntryType;
import jalview.xml.binding.embl.EntryType.Feature;
import jalview.xml.binding.embl.EntryType.Feature.Qualifier;
+import jalview.xml.binding.jalview.JalviewModel;
+import jalview.xml.binding.embl.ROOT;
import jalview.xml.binding.embl.XrefType;
import java.io.File;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import java.util.regex.Pattern;
import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
import javax.xml.bind.JAXBException;
import javax.xml.stream.FactoryConfigurationError;
import javax.xml.stream.XMLInputFactory;
*/
private static final String EMBL_NOT_FOUND_REPLY = "ERROR 12 No entries found.";
- private static final Pattern SPACE_PATTERN = Pattern.compile(" ");
-
public EmblXmlSource()
{
super();
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(is);
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- jalview.xml.binding.embl.ROOT root = (jalview.xml.binding.embl.ROOT) um
- .unmarshal(streamReader);
+ JAXBElement<ROOT> rootElement = um.unmarshal(streamReader, ROOT.class);
+ ROOT root = rootElement.getValue();
/*
* document root contains either "entry" or "entrySet"
SequenceFeature sf = new SequenceFeature(type, desc, begin, end, group);
if (!vals.isEmpty())
{
- StringBuilder sb = new StringBuilder();
- boolean first = true;
for (Entry<String, String> val : vals.entrySet())
{
- if (!first)
- {
- sb.append(";");
- }
- sb.append(val.getKey()).append("=").append(val.getValue());
- first = false;
sf.setValue(val.getKey(), val.getValue());
}
- sf.setAttributes(sb.toString());
}
return sf;
}