JAL-2046 add/delete SequenceFeature operate on dataset if one is defined

[jalview.git] / src / jalview / datamodel / Sequence.java

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index e3746bb..a61f093 100755 (executable)
--- 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;
     }