X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAlignFrame.java;h=092cf477ef0363b8723753141d340ada337e2c39;hb=23d8036c19be1f358742c213d0251163e0ab67a0;hp=e3c42a7d4051e805002eeb0a30acb4743273643d;hpb=4e52fac08f31a714cb9d706178b10364c8f02d69;p=jalview.git

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index e3c42a7..092cf47 100644
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -5442,7 +5442,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
    * Sorts annotations and repaints the alignment
    */
   @Override
-  protected void sortAnnotations()
+  public void sortAnnotations()
   {
     alignPanel.sortAnnotations();
     alignPanel.paintAlignment(false, false);
@@ -5673,13 +5673,19 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
 
   }
 
+  /**
+   * Sets the flag for whether auto-calculated annotations should be shown above
+   * other annotations. If the given value is the same as the current setting,
+   * simply returns false. Otherwise updates the setting, and returns true. If
+   * annotation sort order is currently set to 'Custom', this is changed to
+   * 'None', because 'Custom' ordering ignores all sort options.
+   */
   @Override
-  protected boolean setShowAutoCalculatedAbove(
-          boolean showAutoCalculatedAbove)
+  public boolean setShowAutoCalculatedAbove(boolean b)
   {
-    if (viewport.isShowAutocalculatedAbove() != showAutoCalculatedAbove)
+    if (viewport.isShowAutocalculatedAbove() != b)
     {
-      viewport.setShowAutocalculatedAbove(showAutoCalculatedAbove);
+      viewport.setShowAutocalculatedAbove(b);
 
       /*
        * change CUSTOM annotation ordering to NONE