JAL-1619 AlignedCodonFrame in new alignment should references realigned

[jalview.git] / src / jalview / ws / AWSThread.java

diff --git a/src/jalview/ws/AWSThread.java b/src/jalview/ws/AWSThread.java
index edb56a9..7f05e90 100644 (file)
--- a/src/jalview/ws/AWSThread.java
+++ b/src/jalview/ws/AWSThread.java
@@ -27,8 +27,8 @@ import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
-import jalview.gui.WebserviceInfo;
 import jalview.gui.FeatureRenderer.FeatureRendererSettings;
+import jalview.gui.WebserviceInfo;
 import jalview.util.MessageManager;
 
 public abstract class AWSThread extends Thread
@@ -297,10 +297,11 @@ public abstract class AWSThread extends Thread
       {
         for (int i = 0; i < codonframe.length; i++)
         {
-          if (codonframe[i] != null
-                  && codonframe[i].involvesSequence(alignment[sq]))
+          AlignedCodonFrame acf = codonframe[i];
+          final SequenceI seq = alignment[sq];
+          if (acf != null && acf.involvesSequence(seq))
           {
-            al.addCodonFrame(codonframe[i]);
+            al.addCodonFrame(new AlignedCodonFrame(acf, alignment));
             codonframe[i] = null;
             break;
           }