From cb74c47e3bcfd8b7349da1f25b1f8685db1bca46 Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Tue, 8 Nov 2022 17:39:30 +0000
Subject: [PATCH] JAL-1988 JAL-3772 Fixes highlighted by tests

---
 src/jalview/gui/JvOptionPane.java    |   15 +++++++++++++++
 src/jalview/gui/QuitHandler.java     |   21 +++++++++++----------
 src/jalview/project/Jalview2XML.java |   12 ++++++++++--
 3 files changed, 36 insertions(+), 12 deletions(-)

diff --git a/src/jalview/gui/JvOptionPane.java b/src/jalview/gui/JvOptionPane.java
index b58ea41..6e89fe2 100644
--- a/src/jalview/gui/JvOptionPane.java
+++ b/src/jalview/gui/JvOptionPane.java
@@ -793,6 +793,7 @@ public class JvOptionPane extends JOptionPane
     if (!isInteractiveMode())
     {
       handleResponse(getMockResponse());
+      return;
     }
     // two uses:
     //
@@ -1002,6 +1003,10 @@ public class JvOptionPane extends JOptionPane
   public static int showDialogOnTop(String label, String actionString,
           int JOPTIONPANE_OPTION, int JOPTIONPANE_MESSAGETYPE)
   {
+    if (!isInteractiveMode())
+    {
+      return (int) getMockResponse();
+    }
     // Ensure Jalview window is brought to front (primarily for Quit
     // confirmation window to be visible)
 
@@ -1047,6 +1052,11 @@ public class JvOptionPane extends JOptionPane
           int JOPTIONPANE_MESSAGETYPE, Icon icon, Object[] options,
           Object initialValue, boolean modal, JButton[] buttons)
   {
+    if (!isInteractiveMode())
+    {
+      handleResponse(getMockResponse());
+      return;
+    }
     // Ensure Jalview window is brought to front (primarily for Quit
     // confirmation window to be visible)
 
@@ -1131,6 +1141,11 @@ public class JvOptionPane extends JOptionPane
           Object[] options, Object initialValue, boolean modal,
           JButton[] buttons)
   {
+    if (!isInteractiveMode())
+    {
+      handleResponse(getMockResponse());
+      return null;
+    }
     JButton[] optionsButtons = null;
     Object initialValueButton = null;
     JOptionPane joptionpane = new JOptionPane();
diff --git a/src/jalview/gui/QuitHandler.java b/src/jalview/gui/QuitHandler.java
index e90a2d5..77eed81 100644
--- a/src/jalview/gui/QuitHandler.java
+++ b/src/jalview/gui/QuitHandler.java
@@ -29,10 +29,12 @@ import jalview.util.Platform;
 
 public class QuitHandler
 {
-  private static final int MIN_WAIT_FOR_SAVE = 3000;
+  private static final int MIN_WAIT_FOR_SAVE = 1000;
 
   private static final int MAX_WAIT_FOR_SAVE = 20000;
 
+  private static boolean interactive = true;
+
   public static enum QResponse
   {
     NULL, QUIT, CANCEL_QUIT, FORCE_QUIT
@@ -67,7 +69,7 @@ public class QuitHandler
 
   private static QResponse gotQuitResponse = QResponse.NULL;
 
-  private static QResponse setResponse(QResponse qresponse)
+  protected static QResponse setResponse(QResponse qresponse)
   {
     gotQuitResponse = qresponse;
     return qresponse;
@@ -81,7 +83,7 @@ public class QuitHandler
   public static final Callable<Void> defaultCancelQuit = () -> {
     Console.debug("QuitHandler: (default) Quit action CANCELLED by user");
     // reset
-    setResponse(QResponse.NULL);
+    setResponse(QResponse.CANCEL_QUIT);
     return null;
   };
 
@@ -105,8 +107,6 @@ public class QuitHandler
             defaultCancelQuit);
   }
 
-  private static boolean interactive = true;
-
   public static QResponse getQuitResponse(boolean ui, Callable<Void> okQuit,
           Callable<Void> forceQuit, Callable<Void> cancelQuit)
   {
@@ -147,14 +147,14 @@ public class QuitHandler
     {
       JvOptionPane.newOptionDialog()
               .setResponseHandler(JOptionPane.YES_OPTION, defaultOkQuit)
-              .setResponseHandler(JOptionPane.NO_OPTION, defaultCancelQuit)
+              .setResponseHandler(JOptionPane.NO_OPTION, cancelQuit)
               .showDialogOnTopAsync(
                       new StringBuilder(MessageManager
                               .getString("label.quit_jalview"))
-                                      .append("\n")
-                                      .append(MessageManager.getString(
-                                              "label.unsaved_changes"))
-                                      .toString(),
+                              .append("\n")
+                              .append(MessageManager
+                                      .getString("label.unsaved_changes"))
+                              .toString(),
                       MessageManager.getString("action.quit"),
                       JOptionPane.YES_NO_OPTION,
                       JOptionPane.QUESTION_MESSAGE, null, new Object[]
@@ -168,6 +168,7 @@ public class QuitHandler
     if (got == QResponse.CANCEL_QUIT)
     {
       // reset
+      Console.debug("Cancelling quit.  Resetting response to NULL");
       setResponse(QResponse.NULL);
       // but return cancel
       return QResponse.CANCEL_QUIT;
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 9cec063..c8f9be6 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -625,7 +625,7 @@ public class Jalview2XML
 
     if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
     {
-      int n = 20;
+      int n = debugDelaySave;
       int i = 0;
       while (i < n)
       {
@@ -791,7 +791,7 @@ public class Jalview2XML
 
       if (Cache.getDefault("DEBUG_DELAY_SAVE", false))
       {
-        int n = 20;
+        int n = debugDelaySave;
         int i = 0;
         while (i < n)
         {
@@ -6614,4 +6614,12 @@ public class Jalview2XML
     }
     return true;
   }
+
+  // used for debugging and tests
+  private static int debugDelaySave = 20;
+
+  public static void setDebugDelaySave(int n)
+  {
+    debugDelaySave = n;
+  }
 }
-- 
1.7.10.2