JAL-2255 Bug fix

[jalview.git] / src / jalview / gui / AlignFrame.java

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 445e967..507bfab 100644 (file)
--- 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);
@@ -5705,23 +5713,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
     ColourMenuHelper.setColourSelected(colourMenu, schemeName);
   }
-
-  /**
-   * Disable inapplicable items in the Select menu when it is clicked
-   */
-  @Override
-  protected void configureSelectMenu()
-  {
-    createGroup.setEnabled(false);
-    unGroup.setEnabled(false);
-    SequenceGroup sg = viewport.getSelectionGroup();
-    if (sg != null)
-    {
-      List<SequenceGroup> groups = viewport.getAlignment().getGroups();
-      createGroup.setEnabled(groups == null || !groups.contains(sg));
-      unGroup.setEnabled(groups != null && groups.contains(sg));
-    }
-  }
 }
 
 class PrintThread extends Thread