JAL-1577 rebuild menus when secondary structure manually updated

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index bb311ef..60c182e 100755 (executable)
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -351,7 +351,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
     }
     else
-    // HELIX OR SHEET
+    // HELIX, SHEET or STEM
     {
       char type = 0;
       String symbol = "\u03B1";
@@ -412,9 +412,10 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       }
     }
+
     av.getAlignment().validateAnnotation(aa[activeRow]);
     ap.alignmentChanged();
-
+    ap.alignFrame.setMenusForViewport();
     adjustPanelHeight();
     repaint();