From 2b5c2dd88dd2f087fdf61427e59704d7bf05d627 Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Wed, 7 Jun 2023 14:02:11 +0100
Subject: [PATCH] JAL-4195 tidy up desktop instances after creating them

---
 src/jalview/gui/Desktop.java        |   13 +++++++++++++
 test/jalview/bin/CommandsTest.java  |   19 +++++++++++++------
 test/jalview/bin/CommandsTest2.java |    5 ++---
 3 files changed, 28 insertions(+), 9 deletions(-)

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 6f2faae..1fcc591 100644
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -3571,4 +3571,17 @@ public class Desktop extends jalview.jbgui.GDesktop
       jalview.bin.Console.debug(Cache.getStackTraceString(e));
     }
   }
+
+  /**
+   * closes the current instance window, disposes and forgets about it.
+   */
+  public static void closeDesktop()
+  {
+    if (Desktop.instance != null) {
+      Desktop.instance.closeAll_actionPerformed(null);
+      Desktop.instance.setVisible(false);
+      Desktop.instance.dispose();
+      Desktop.instance = null;
+    }
+  }
 }
diff --git a/test/jalview/bin/CommandsTest.java b/test/jalview/bin/CommandsTest.java
index b4c927b..61892df 100644
--- a/test/jalview/bin/CommandsTest.java
+++ b/test/jalview/bin/CommandsTest.java
@@ -49,8 +49,15 @@ public class CommandsTest
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    if (Desktop.instance != null)
-      Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.closeDesktop();
+  }
+  
+  public static void callJalviewMain(String[] args) {
+    if (Jalview.getInstance()!=null) {
+      Jalview.getInstance().doMain(args);
+    } else {
+      Jalview.main(args);
+    }
   }
 
   /* --setprops is currently disabled so this test won't work
@@ -71,7 +78,7 @@ public class CommandsTest
           int numFrames, String[] sequences)
   {
     String[] args = (cmdLine + " --gui").split("\\s+");
-    Jalview.main(args);
+    callJalviewMain(args);
     Commands cmds = Jalview.getInstance().getCommands();
     Assert.assertNotNull(cmds);
     Assert.assertEquals(cmds.commandArgsProvided(), cmdArgs,
@@ -111,7 +118,7 @@ public class CommandsTest
   {
     cleanupFiles(filenames);
     String[] args = (cmdLine + " --gui").split("\\s+");
-    Jalview.main(args);
+    callJalviewMain(args);
     Commands cmds = Jalview.getInstance().getCommands();
     Assert.assertNotNull(cmds);
     File lastFile = null;
@@ -139,7 +146,7 @@ public class CommandsTest
   {
     cleanupFiles(filenames);
     String[] args = (cmdLine + " --gui").split("\\s+");
-    Jalview.main(args);
+    callJalviewMain(args);
     Commands cmds = Jalview.getInstance().getCommands();
     Assert.assertNotNull(cmds);
     File lastFile = null;
@@ -297,7 +304,7 @@ public class CommandsTest
           String[] nonfilenames)
   {
     String[] args = (cmdLine + " --gui").split("\\s+");
-    Jalview.main(args);
+    callJalviewMain(args);
     Commands cmds = Jalview.getInstance().getCommands();
     Assert.assertNotNull(cmds);
     for (String filename : filenames)
diff --git a/test/jalview/bin/CommandsTest2.java b/test/jalview/bin/CommandsTest2.java
index 0a47700..0c2071a 100644
--- a/test/jalview/bin/CommandsTest2.java
+++ b/test/jalview/bin/CommandsTest2.java
@@ -51,8 +51,7 @@ public class CommandsTest2
   @AfterMethod(alwaysRun = true)
   public void tearDown()
   {
-    if (Desktop.instance != null)
-      Desktop.instance.closeAll_actionPerformed(null);
+    Desktop.closeDesktop();
   }
 
   @Test(
@@ -65,7 +64,7 @@ public class CommandsTest2
   {
     String[] args = cmdLine.split("\\s+");
 
-    Jalview.main(args);
+    CommandsTest.callJalviewMain(args);
     try
     {
       // sleep for slow build server to open annotations and viewer windows
-- 
1.7.10.2