*/
package jalview.io.vamsas;
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceI;
+import jalview.io.VamsasAppDatastore;
+import jalview.util.UrlLink;
+
import java.util.Enumeration;
+import java.util.Iterator;
import java.util.Vector;
import uk.ac.vamsas.objects.core.DataSetAnnotations;
import uk.ac.vamsas.objects.core.Score;
import uk.ac.vamsas.objects.core.Seg;
import uk.ac.vamsas.objects.utils.Properties;
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceFeature;
-import jalview.datamodel.SequenceI;
-import jalview.io.VamsasAppDatastore;
-import jalview.util.UrlLink;
/**
* @author JimP
doJvUpdate();
}
+ @Override
public void addToDocument()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
dataset.addDataSetAnnotations(dsa);
}
+ @Override
public void addFromDocument()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
bindjvvobj(sf, dsa);
}
+ @Override
public void conflict()
{
log.warn("Untested sequencefeature conflict code");
addToDocument(); // and create a new feature in the document
}
+ @Override
public void updateToDoc()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
}
+ @Override
public void updateFromDoc()
{
DataSetAnnotations dsa = (DataSetAnnotations) vobj;
.debug("About to destroy complex annotation in vamsas document mapped to sequence feature ("
+ dsa.getVorbaId() + ")");
}
- dsa.setSeg(new Seg[]
- { vSeg });
+ dsa.setSeg(new Seg[] { vSeg });
dsa.setDescription(feature.getDescription());
dsa.setStatus(feature.getStatus());
if (feature.links != null && feature.links.size() > 0)
{
for (int i = 0, iSize = feature.links.size(); i < iSize; i++)
{
- String link = (String) feature.links.elementAt(i);
+ String link = feature.links.elementAt(i);
UrlLink ulink = new UrlLink(link);
if (ulink.isValid())
{
if (!Float.isNaN(feature.getScore()))
{
Score fscore = new Score();
- dsa.setScore(new Score[]
- { fscore });
+ dsa.setScore(new Score[] { fscore });
fscore.setContent(feature.getScore());
fscore.setName(feature.getType());
}
if (feature.otherDetails != null)
{
- Enumeration iter = feature.otherDetails.keys();
+ Iterator<String> iter = feature.otherDetails.keySet().iterator();
Vector props = dsa.getPropertyAsReference();
- while (iter.hasMoreElements())
+ while (iter.hasNext())
{
- String key = (String) iter.nextElement();
+ String key = iter.next();
if (!key.equalsIgnoreCase("score")
&& !key.equalsIgnoreCase("status"))
{