From b7be944577dabe7c497947903c83d14f46f14b1d Mon Sep 17 00:00:00 2001
From: BobHanson <hansonr@stolaf.edu>
Date: Mon, 1 Jun 2020 16:41:54 -0500
Subject: [PATCH] JAL-3262 from JAL-3253-applet JalviewApp integration

---
 src/jalview/gui/AlignFrame.java |   19 ++++++++++++++-----
 1 file changed, 14 insertions(+), 5 deletions(-)

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 7818748..89628e7 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -4820,11 +4820,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       }
       if (isAnnotation)
       {
-
-        alignPanel.adjustAnnotationHeight();
-        viewport.updateSequenceIdColours();
-        buildSortByAnnotationScoresMenu();
-        alignPanel.paintAlignment(true, true);
+        updateForAnnotations();
       }
     } catch (Exception ex)
     {
@@ -4853,6 +4849,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
   }
 
   /**
+   * Do all updates necessary after an annotation file such as jnet. Also called
+   * from Jalview.loadAppletParams for "annotations", "jnetFile"
+   */
+
+  public void updateForAnnotations()
+  {
+    alignPanel.adjustAnnotationHeight();
+    viewport.updateSequenceIdColours();
+    buildSortByAnnotationScoresMenu();
+    alignPanel.paintAlignment(true, true);
+  }
+
+  /**
    * Method invoked by the ChangeListener on the tabbed pane, in other words
    * when a different tabbed pane is selected by the user or programmatically.
    */
-- 
1.7.10.2