From ab980b5a5576787c34f6b5ea4e31c11ffda286bd Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Wed, 25 Oct 2023 11:16:01 +0100
Subject: [PATCH] JAL-4312 call AlignFrame.setAnnotationsVisibility on AWT
 thread from Commands

---
 src/jalview/bin/Commands.java |   49 +++++++++++++++++++++++++++++++----------
 1 file changed, 37 insertions(+), 12 deletions(-)

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index e02d132..a092cd6 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -13,6 +13,8 @@ import java.util.List;
 import java.util.Locale;
 import java.util.Map;
 
+import javax.swing.SwingUtilities;
+
 import jalview.analysis.AlignmentUtils;
 import jalview.api.structures.JalviewStructureDisplayI;
 import jalview.bin.Jalview.ExitCode;
@@ -361,28 +363,51 @@ public class Commands
             }
           }
 
+          
           // Show secondary structure annotations?
           boolean showSSAnnotations = avm.getFromSubValArgOrPref(
                   Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
                   "STRUCT_FROM_PDB", true);
-          af.setAnnotationsVisibility(showSSAnnotations, true, false);
-
+          
           // Show sequence annotations?
           boolean showAnnotations = avm.getFromSubValArgOrPref(
                   Arg.SHOWANNOTATIONS, av.getSubVals(), null,
                   "SHOW_ANNOTATIONS", true);
-          af.setAnnotationsVisibility(showAnnotations, false, true);
+          
+          boolean hideTFrows = (avm.getBoolean(Arg.NOTEMPFAC));
+          final AlignFrame _af = af;
+          // many of jalview's format/layout methods are only thread safe on the swingworker thread.
+          // all these methods should be on the alignViewController so it can coordinate such details
+          try
+          {
+            SwingUtilities.invokeAndWait(new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                _af.setAnnotationsVisibility(showSSAnnotations, true,
+                        false);
 
-          // show temperature factor annotations?
-          if (avm.getBoolean(Arg.NOTEMPFAC))
+                _af.setAnnotationsVisibility(showAnnotations, false, true);
+
+                // show temperature factor annotations?
+                if (hideTFrows)
+                {
+                  // do this better (annotation types?)
+                  List<String> hideThese = new ArrayList<>();
+                  hideThese.add("Temperature Factor");
+                  hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
+                  AlignmentUtils.showOrHideSequenceAnnotations(
+                          _af.getCurrentView().getAlignment(), hideThese,
+                          null, false, false);
+                }
+              }
+            });
+          } catch (Exception x)
           {
-            // do this better (annotation types?)
-            List<String> hideThese = new ArrayList<>();
-            hideThese.add("Temperature Factor");
-            hideThese.add(AlphaFoldAnnotationRowBuilder.LABEL);
-            AlignmentUtils.showOrHideSequenceAnnotations(
-                    af.getCurrentView().getAlignment(), hideThese, null,
-                    false, false);
+            Console.warn(
+                    "Unexpected exception adjusting annotation row visibility.",
+                    x);
           }
 
           // wrap alignment? do this last for formatting reasons
-- 
1.7.10.2