JAL-1264 reinstate Show annotations menu item

[jalview.git] / src / jalview / gui / Jalview2XML.java

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index 8beb26f..2528841 100644 (file)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -2263,6 +2263,13 @@ public class Jalview2XML
     int height = (int) (dnaFrame.getBounds().getHeight()
             + proteinFrame.getBounds().getHeight() + 50);
     Desktop.addInternalFrame(splitFrame, title, width, height);
+
+    /*
+     * And compute cDNA consensus (couldn't do earlier with consensus as
+     * mappings were not yet present)
+     */
+    proteinFrame.viewport.alignmentChanged(proteinFrame.alignPanel);
+
     return splitFrame;
   }
 
@@ -3452,7 +3459,7 @@ public class Jalview2XML
                       (OutOfMemoryError) ex.getCause());
               if (sview != null && sview.isVisible())
               {
-                sview.closeViewer();
+                sview.closeViewer(false);
                 sview.setVisible(false);
                 sview.dispose();
               }