JAL-2046 setSequenceFeature contract implementation and warning message

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

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index fbe3670..5bfdb04 100755 (executable)
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -293,16 +293,20 @@ public class Sequence extends ASequence implements SequenceI
     }
   }
 
-  /**
-   * DOCUMENT ME!
-   * 
-   * @param v
-   *          DOCUMENT ME!
-   */
+
   @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
@@ -1056,31 +1060,24 @@ public class Sequence extends ASequence implements SequenceI
   @Override
   public SequenceI deriveSequence()
   {
-    SequenceI seq = new Sequence(this);
-    if (datasetSequence != null)
-    {
-      // duplicate current sequence with same dataset
-      seq.setDatasetSequence(datasetSequence);
-    }
-    else
+    Sequence seq=null;
+    if (datasetSequence == null)
     {
       if (isValidDatasetSequence())
       {
         // Use this as dataset sequence
+        seq = new Sequence(getName(), "", 1, -1);
         seq.setDatasetSequence(this);
+        seq.initSeqFrom(this, getAnnotation());
+        return seq;
       }
       else
       {
         // Create a new, valid dataset sequence
-        SequenceI ds = seq;
-        ds.setSequence(AlignSeq.extractGaps(
-                jalview.util.Comparison.GapChars, new String(sequence)));
-        setDatasetSequence(ds);
-        ds.setSequenceFeatures(getSequenceFeatures());
-        seq = this; // and return this sequence as the derived sequence.
+       createDatasetSequence();
       }
     }
-    return seq;
+    return new Sequence(this);
   }
 
   /*