X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequence.java;h=a61f0939e22f27f652aad0d07a7179b4c349449d;hb=d645ed1944459b6271dea2a8511a1e0f4f997530;hp=e3746bb2f5482ed1d5dce85bb2fb9b91b9227f38;hpb=f13923193668b9ad0a28fccc8a0d2432c73c6ff4;p=jalview.git

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index e3746bb..a61f093 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -297,13 +297,26 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public void setSequenceFeatures(SequenceFeature[] features)
   {
-    sequenceFeatures = features;
+    if (datasetSequence == null)
+    {
+      sequenceFeatures = features;
+    }
+    else
+    {
+      System.err
+              .println("Warning: JAL-2046 side effect ? Possible implementation error: overwriting dataset sequence features by setting sequence features on alignment");
+      datasetSequence.setSequenceFeatures(features);
+    }
   }
 
   @Override
   public synchronized void addSequenceFeature(SequenceFeature sf)
   {
-    // TODO add to dataset sequence instead if there is one?
+    if (sequenceFeatures==null && datasetSequence != null)
+    {
+      datasetSequence.addSequenceFeature(sf);
+      return;
+    }
     if (sequenceFeatures == null)
     {
       sequenceFeatures = new SequenceFeature[0];
@@ -329,6 +342,9 @@ public class Sequence extends ASequence implements SequenceI
   {
     if (sequenceFeatures == null)
     {
+      if (datasetSequence!=null) {
+    	  datasetSequence.deleteFeature(sf);
+      }
       return;
     }