From: Jim Procter <jprocter@issues.jalview.org>
Date: Tue, 5 Apr 2016 17:31:32 +0000 (+0100)
Subject: JAL-2046 setSequenceFeature contract implementation and warning message
X-Git-Tag: Release_2_10_0~249^2~31^2~6
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=6819fa797b45769bb38a80230e5961e09582ed9e

JAL-2046 setSequenceFeature contract implementation and warning message
---

diff --git a/src/jalview/datamodel/Sequence.java b/src/jalview/datamodel/Sequence.java
index e3746bb..5bfdb04 100755
--- a/src/jalview/datamodel/Sequence.java
+++ b/src/jalview/datamodel/Sequence.java
@@ -297,7 +297,16 @@ 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