*/
package jalview.analysis;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
+
public class SeqsetUtils
{
sfeat.addElement(sfarray[i]);
}
}
- sqinfo.put("SeqFeatures", sfeat);
- sqinfo.put("PdbId", (seq.getPDBId() != null) ? seq.getPDBId()
- : new Vector<PDBEntry>());
- sqinfo.put("datasetSequence",
- (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
- : new Sequence("THISISAPLACEHOLDER", ""));
+ if (seq.getDatasetSequence() == null)
+ {
+ sqinfo.put("SeqFeatures", sfeat);
+ sqinfo.put("PdbId",
+ (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
+ : new Vector<PDBEntry>());
+ }
+ else
+ {
+ sqinfo.put("datasetSequence",
+ (seq.getDatasetSequence() != null) ? seq.getDatasetSequence()
+ : new Sequence("THISISAPLACEHOLDER", ""));
+ }
return sqinfo;
}
&& !(seqds.getName().equals("THISISAPLACEHOLDER") && seqds
.getLength() == 0))
{
+ if (sfeatures != null)
+ {
+ System.err
+ .println("Implementation error: setting dataset sequence for a sequence which has sequence features.\n\tDataset sequence features will not be visible.");
+ }
sq.setDatasetSequence(seqds);
}