X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;fp=src%2Fjalview%2Fgui%2FAlignFrame.java;h=507bfab40c2e00bae51d9702dc3aca3f46002b80;hb=71b7dc2dbc920391e3209bde9e915dd3436871f3;hp=ab1ac0e1b533b8a208d859c7996dd24fb6e5d7c5;hpb=2d5838594f5ac09384c684209c16961f47b42af5;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index ab1ac0e..507bfab 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -2750,6 +2750,14 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
      */
     newap.av.replaceMappings(viewport.getAlignment());
 
+    /*
+     * start up cDNA consensus (if applicable) now mappings are in place
+     */
+    if (newap.av.initComplementConsensus())
+    {
+      newap.refresh(true); // adjust layout of annotations
+    }
+
     newap.av.viewName = getNewViewName(viewTitle);
 
     addAlignmentPanel(newap, true);