From 04cefeebe4d5267638319c74fe68b8b9cc0bf37a Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Thu, 2 Nov 2023 19:43:01 +0000
Subject: [PATCH] JAL-4217 wrap progress bar creation in an invokeLater to
 avoid setFont deadlock with other ops

---
 src/jalview/bin/Commands.java |   58 ++++++++++++++++++++++++++---------------
 1 file changed, 37 insertions(+), 21 deletions(-)

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index a092cd6..2794b02 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -196,7 +196,7 @@ public class Commands
     if (avm.containsArg(Arg.APPEND) || avm.containsArg(Arg.OPEN))
     {
       commandArgsProvided = true;
-      long progress = -1;
+      final long progress = System.currentTimeMillis();
 
       boolean first = true;
       boolean progressBarSet = false;
@@ -222,10 +222,18 @@ public class Commands
           first = false;
           if (!headless && desktop != null)
           {
-            desktop.setProgressBar(
-                    MessageManager.getString(
-                            "status.processing_commandline_args"),
-                    progress = System.currentTimeMillis());
+            SwingUtilities.invokeLater(new Runnable()
+            {
+              @Override
+              public void run()
+              {
+                desktop.setProgressBar(
+                        MessageManager.getString(
+                                "status.processing_commandline_args"),
+                        progress);
+
+              }
+            });
             progressBarSet = true;
           }
         }
@@ -363,25 +371,27 @@ public class Commands
             }
           }
 
-          
           // Show secondary structure annotations?
           boolean showSSAnnotations = avm.getFromSubValArgOrPref(
                   Arg.SHOWSSANNOTATIONS, av.getSubVals(), null,
                   "STRUCT_FROM_PDB", true);
-          
+
           // Show sequence annotations?
           boolean showAnnotations = avm.getFromSubValArgOrPref(
                   Arg.SHOWANNOTATIONS, av.getSubVals(), null,
                   "SHOW_ANNOTATIONS", 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
+          // 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()
               {
@@ -433,9 +443,11 @@ public class Commands
         {
           Console.debug(
                   "Opening '" + openFile + "' in existing alignment frame");
+
           DataSourceType dst = HttpUtils.startsWithHttpOrHttps(openFile)
                   ? DataSourceType.URL
                   : DataSourceType.FILE;
+
           FileLoader fileLoader = new FileLoader(!headless);
           fileLoader.LoadFile(af.getCurrentView(), openFile, dst, null,
                   false);
@@ -464,11 +476,14 @@ public class Commands
     // open the structure (from same PDB file or given PDBfile)
     if (!avm.getBoolean(Arg.NOSTRUCTURE))
     {
+
       AlignFrame af = afMap.get(id);
       if (avm.containsArg(Arg.STRUCTURE))
       {
         commandArgsProvided = true;
-        for (ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
+        for (
+
+        ArgValue av : avm.getArgValueList(Arg.STRUCTURE))
         {
           argParser.setStructureFilename(null);
           String val = av.getValue();
@@ -835,6 +850,7 @@ public class Commands
 
     if (wrap)
     {
+
       AlignFrame af = afMap.get(id);
       if (af != null)
       {
@@ -846,16 +862,16 @@ public class Commands
     boolean doShading = avm.getBoolean(Arg.TEMPFAC_SHADING);
     if (doShading)
     {
-      AlignFrame af = afMap.get(id);
-      for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
-              .findAnnotation(PDBChain.class.getName().toString()))
-      {
-        AnnotationColourGradient acg = new AnnotationColourGradient(aa,
-                af.alignPanel.av.getGlobalColourScheme(), 0);
-        acg.setSeqAssociated(true);
-        af.changeColour(acg);
-        Console.info("Changed colour " + acg.toString());
-      }
+    AlignFrame af = afMap.get(id);
+    for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+            .findAnnotation(PDBChain.class.getName().toString()))
+    {
+      AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+              af.alignPanel.av.getGlobalColourScheme(), 0);
+      acg.setSeqAssociated(true);
+      af.changeColour(acg);
+      Console.info("Changed colour " + acg.toString());
+    }
     }
     */
 
-- 
1.7.10.2