JAL-2046 fix: patched SeqsetUtils so sequence features aren’t duplicated when reinsta...

[jalview.git] / src / jalview / analysis / SeqsetUtils.java

diff --git a/src/jalview/analysis/SeqsetUtils.java b/src/jalview/analysis/SeqsetUtils.java
index c23f03c..b0ecfde 100755 (executable)
--- a/src/jalview/analysis/SeqsetUtils.java
+++ b/src/jalview/analysis/SeqsetUtils.java
@@ -20,15 +20,15 @@
  */
 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
 {
 
@@ -59,12 +59,19 @@ public class SeqsetUtils
         sfeat.addElement(sfarray[i]);
       }
     }
-    sqinfo.put("SeqFeatures", sfeat);
-    sqinfo.put("PdbId", (seq.getAllPDBEntries() != null) ? seq.getAllPDBEntries()
-            : new Vector<PDBEntry>());
-    sqinfo.put("datasetSequence",
+    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;
   }
 
@@ -128,6 +135,11 @@ public class SeqsetUtils
             && !(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);
     }