+ }
+
+ ///
+ // Create the alignment object from the sequence set
+ /////////////////////////////////
+ jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
+ .size()];
+
+ tmpseqs.toArray(orderedSeqs);
+
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
+ orderedSeqs);
+
+ /// Add the alignment properties
+ for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
+ {
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
+ al.setProperty(ssp.getKey(), ssp.getValue());
+ }
+
+ ///
+ // SequenceFeatures are added to the DatasetSequence,
+ // so we must create or recover the dataset before loading features
+ /////////////////////////////////
+ if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
+ {
+ // older jalview projects do not have a dataset id.
+ al.setDataset(null);
+ }
+ else
+ {
+ recoverDatasetFor(vamsasSet, al);
+ }
+ /////////////////////////////////
+
+ Hashtable pdbloaded = new Hashtable();
+ if (!multipleView)
+ {
+ for (int i = 0; i < vamsasSeq.length; i++)
+ {
+ if (JSEQ[i].getFeaturesCount() > 0)
+ {
+ Features[] features = JSEQ[i].getFeatures();
+ for (int f = 0; f < features.length; f++)
+ {
+ jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
+ features[f].getType(), features[f].getDescription(),
+ features[f].getStatus(), features[f].getBegin(),
+ features[f].getEnd(), features[f].getFeatureGroup());
+
+ sf.setScore(features[f].getScore());
+ for (int od = 0; od < features[f].getOtherDataCount(); od++)