From a800086bf169fc6495fef3effa56338f5cff4804 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 11 Jan 2023 13:04:47 +0000
Subject: [PATCH] JAL-1988 JAL-3772 Mark the _default_ STARTUP_FILE as 'all
 saved' after initial opening

---
 src/jalview/bin/Jalview.java |   20 +++++++++++++++++---
 1 file changed, 17 insertions(+), 3 deletions(-)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 0ec9889..9472fb3 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -877,6 +877,8 @@ public class Jalview
      * @j2sIgnore
      */
     {
+      boolean defaultStartupFile = Cache.getDefault("STARTUP_FILE",
+              null) == null;
       file = Cache.getDefault("STARTUP_FILE",
               Cache.getDefault("www.jalview.org", "https://www.jalview.org")
                       + "/examples/exampleFile_2_7.jvp");
@@ -890,6 +892,7 @@ public class Jalview
         file.replace("2_7.jar", "2_7.jvp");
         // and remove the stale setting
         Cache.removeProperty("STARTUP_FILE");
+        defaultStartupFile = true;
       }
 
       protocol = AppletFormatAdapter.checkProtocol(file);
@@ -911,6 +914,11 @@ public class Jalview
 
       startUpAlframe = fileLoader.LoadFileWaitTillLoaded(file, protocol,
               format);
+      if (defaultStartupFile)
+      {
+        Console.debug("Resetting up-to-date flag for startup file");
+        startUpAlframe.getViewport().setSavedUpToDate(true);
+      }
       // extract groovy arguments before anything else.
     }
 
@@ -1125,22 +1133,27 @@ public class Jalview
   private static boolean setFlatLookAndFeel()
   {
     boolean set = false;
-    if (Platform.isMac()) {
+    if (Platform.isMac())
+    {
       try
       {
-        UIManager.setLookAndFeel("com.formdev.flatlaf.themes.FlatMacLightLaf");
+        UIManager.setLookAndFeel(
+                "com.formdev.flatlaf.themes.FlatMacLightLaf");
         set = true;
+        Console.debug("*** Loaded FlatMacLightLaf");
       } catch (ClassNotFoundException | InstantiationException
               | IllegalAccessException | UnsupportedLookAndFeelException e)
       {
         Console.debug("Exception loading FlatMacLightLaf", e);
       }
     }
-    if (!set) {
+    if (!set)
+    {
       try
       {
         UIManager.setLookAndFeel("com.formdev.flatlaf.FlatLightLaf");
         set = true;
+        Console.debug("*** Loaded FlatLightLaf");
       } catch (ClassNotFoundException | InstantiationException
               | IllegalAccessException | UnsupportedLookAndFeelException e)
       {
@@ -1158,6 +1171,7 @@ public class Jalview
         if (SystemInfo.isMacFullWindowContentSupported
                 && Desktop.desktop != null)
         {
+          Console.debug("Setting transparent title bar");
           Desktop.desktop.getRootPane()
                   .putClientProperty("apple.awt.fullWindowContent", true);
           Desktop.desktop.getRootPane()
-- 
1.7.10.2