package jalview.io.vamsas;
import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.VamsasAppDatastore;
+import java.util.List;
+
import uk.ac.vamsas.objects.core.DataSet;
import uk.ac.vamsas.objects.core.DbRef;
import uk.ac.vamsas.objects.core.Sequence;
doJvUpdate();
}
+ @Override
public void addFromDocument()
{
Sequence vseq = (Sequence) vobj;
modified = true;
}
+ @Override
public void updateFromDoc()
{
Sequence sq = (Sequence) vobj;
*/
private boolean updateSqFeatures()
{
- boolean modified = false;
+ boolean changed = false;
SequenceI sq = (SequenceI) jvobj;
// add or update any new features/references on dataset sequence
- if (sq.getSequenceFeatures() != null)
+ List<SequenceFeature> sfs = sq.getSequenceFeatures();
+ for (SequenceFeature sf : sfs)
{
- int sfSize = sq.getSequenceFeatures().length;
-
- for (int sf = 0; sf < sfSize; sf++)
- {
- modified |= new jalview.io.vamsas.Sequencefeature(datastore,
- (jalview.datamodel.SequenceFeature) sq
- .getSequenceFeatures()[sf], dataset,
- (Sequence) vobj).docWasUpdated();
- }
+ changed |= new jalview.io.vamsas.Sequencefeature(datastore, sf,
+ dataset, (Sequence) vobj).docWasUpdated();
}
- return modified;
+
+ return changed;
}
+ @Override
public void addToDocument()
{
SequenceI sq = (SequenceI) jvobj;
return modifiedtheseq;
}
+ @Override
public void conflict()
{
log.warn("Conflict in dataset sequence update to document. Overwriting document");
boolean modified = false;
+ @Override
public void updateToDoc()
{
SequenceI sq = (SequenceI) jvobj;