From 4c007a518fc7e2fdaa863f16cb715f8e45e6cfbf Mon Sep 17 00:00:00 2001
From: Ben Soares <b.soares@dundee.ac.uk>
Date: Wed, 2 Nov 2022 14:34:11 +0000
Subject: [PATCH] JAL-1988 JAL-3772 Moving packages to somewhere more obvious
 (jbgui -> gui)

---
 src/jalview/bin/Jalview.java                |    4 ++--
 src/jalview/{jbgui => gui}/APQHandlers.java |    4 ++--
 src/jalview/gui/Desktop.java                |    3 +--
 src/jalview/{jbgui => gui}/QuitHandler.java |    5 +----
 src/jalview/jbgui/GDesktop.java             |    4 ++--
 5 files changed, 8 insertions(+), 12 deletions(-)
 rename src/jalview/{jbgui => gui}/APQHandlers.java (95%)
 rename src/jalview/{jbgui => gui}/QuitHandler.java (99%)

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 546e931..b5e1958 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -61,6 +61,8 @@ import jalview.ext.so.SequenceOntology;
 import jalview.gui.AlignFrame;
 import jalview.gui.Desktop;
 import jalview.gui.PromptUserConfig;
+import jalview.gui.QuitHandler;
+import jalview.gui.QuitHandler.QResponse;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.BioJsHTMLOutput;
 import jalview.io.DataSourceType;
@@ -73,8 +75,6 @@ import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
 import jalview.io.gff.SequenceOntologyFactory;
-import jalview.jbgui.QuitHandler;
-import jalview.jbgui.QuitHandler.QResponse;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.util.ChannelProperties;
diff --git a/src/jalview/jbgui/APQHandlers.java b/src/jalview/gui/APQHandlers.java
similarity index 95%
rename from src/jalview/jbgui/APQHandlers.java
rename to src/jalview/gui/APQHandlers.java
index 12ce1ba..00ec217 100644
--- a/src/jalview/jbgui/APQHandlers.java
+++ b/src/jalview/gui/APQHandlers.java
@@ -18,7 +18,7 @@
  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
-package jalview.jbgui;
+package jalview.gui;
 
 import com.formdev.flatlaf.extras.FlatDesktop;
 import com.formdev.flatlaf.extras.FlatDesktop.Action;
@@ -33,7 +33,7 @@ public class APQHandlers
 
   public static boolean setQuit = false;
 
-  public static boolean setAPQHandlers(GDesktop desktop)
+  public static boolean setAPQHandlers(Desktop desktop)
   {
     if (Platform.isJS())
     {
diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 72c9106..94145bd 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -105,6 +105,7 @@ import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.gui.ImageExporter.ImageWriterI;
+import jalview.gui.QuitHandler.QResponse;
 import jalview.io.BackupFiles;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -118,8 +119,6 @@ import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
 import jalview.jbgui.GSplitFrame;
 import jalview.jbgui.GStructureViewer;
-import jalview.jbgui.QuitHandler;
-import jalview.jbgui.QuitHandler.QResponse;
 import jalview.project.Jalview2XML;
 import jalview.structure.StructureSelectionManager;
 import jalview.urls.IdOrgSettings;
diff --git a/src/jalview/jbgui/QuitHandler.java b/src/jalview/gui/QuitHandler.java
similarity index 99%
rename from src/jalview/jbgui/QuitHandler.java
rename to src/jalview/gui/QuitHandler.java
index 7b5be98..75ff0b0 100644
--- a/src/jalview/jbgui/QuitHandler.java
+++ b/src/jalview/gui/QuitHandler.java
@@ -1,4 +1,4 @@
-package jalview.jbgui;
+package jalview.gui;
 
 import java.io.File;
 import java.util.List;
@@ -22,9 +22,6 @@ import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
 import jalview.io.BackupFiles;
 import jalview.project.Jalview2XML;
 import jalview.util.MessageManager;
diff --git a/src/jalview/jbgui/GDesktop.java b/src/jalview/jbgui/GDesktop.java
index 3343c88..b0079b4 100755
--- a/src/jalview/jbgui/GDesktop.java
+++ b/src/jalview/jbgui/GDesktop.java
@@ -32,6 +32,7 @@ import javax.swing.JMenuItem;
 
 import jalview.api.AlignmentViewPanel;
 import jalview.bin.Cache;
+import jalview.gui.APQHandlers;
 import jalview.gui.Desktop;
 import jalview.io.FileFormatException;
 import jalview.util.MessageManager;
@@ -141,7 +142,6 @@ public class GDesktop extends JFrame
    */
   private void jbInit() throws Exception
   {
-    boolean apqHandlersSet = false;
     /**
      * APQHandlers sets handlers for About, Preferences and Quit actions
      * peculiar to macOS's application menu. APQHandlers will check to see if a
@@ -149,7 +149,7 @@ public class GDesktop extends JFrame
      */
     try
     {
-      apqHandlersSet = APQHandlers.setAPQHandlers(this);
+      APQHandlers.setAPQHandlers((Desktop) this);
     } catch (Exception e)
     {
       System.out.println("Cannot set APQHandlers");
-- 
1.7.10.2