From 09eebd8c6997a33049084e307078717cc1a693a6 Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 24 Jan 2023 07:48:54 +0000
Subject: [PATCH] =?utf8?q?JAL-629=20don=E2=80=99t=20carry=20on=20Jalview.mai?=
 =?utf8?q?n=20if=20we=E2=80=99ve=20already=20processed=20command=20line=20ar?=
 =?utf8?q?gs=20another=20way?=
MIME-Version: 1.0
Content-Type: text/plain; charset=utf8
Content-Transfer-Encoding: 8bit

---
 src/jalview/bin/Commands.java |   31 ++++++++++++++++++++++---------
 src/jalview/bin/Jalview.java  |    5 ++++-
 2 files changed, 26 insertions(+), 10 deletions(-)

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index 289d962..61ee1be 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -48,11 +48,11 @@ public class Commands
 
   private Map<String, AlignFrame> afMap;
 
-  public static void processArgs(ArgParser ap, boolean h)
+  public static boolean processArgs(ArgParser ap, boolean h)
   {
     argParser = ap;
     headless = h;
-
+    boolean argsWereParsed = false;
     if (headless)
     {
       System.setProperty("java.awt.headless", "true");
@@ -73,14 +73,24 @@ public class Commands
           cmds.processLinked(id);
         }
         cmds.processImages(id);
+        argsWereParsed |= cmds.wereParsed();
       }
 
     }
     if (argParser.getBool(Arg.QUIT))
     {
       Jalview.getInstance().quit();
-      // Desktop.instance.quit();
+      return true;
     }
+    // carry on with jalview.bin.Jalview
+    return argsWereParsed;
+  }
+
+  boolean argsWereParsed = false;
+
+  private boolean wereParsed()
+  {
+    return argsWereParsed;
   }
 
   public Commands()
@@ -328,12 +338,15 @@ public class Commands
           Console.error("Could not open any files in headless mode");
           System.exit(1);
         }
-      }
-      else
-      {
-        Console.warn("No more files to open");
-        if (desktop != null)
-          desktop.setProgressBar(null, progress);
+        // TOREMOVE COMMENT
+        // @Ben assumed this was the GUI version of above, rather then the
+        // first==false state
+        else
+        {
+          Console.warn("No more files to open");
+          if (desktop != null)
+            desktop.setProgressBar(null, progress);
+        }
       }
 
     }
diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 1f01125..6238c7d 100755
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -565,7 +565,10 @@ public class Jalview
 
     if (argparser.isSet(Arg.HEADLESS))
       headless = argparser.getBool(Arg.HEADLESS);
-    Commands.processArgs(argparser, headless);
+    if (Commands.processArgs(argparser, headless))
+    {
+      System.exit(1);
+    }
 
     String file = null, data = null;
     FileFormatI format = null;
-- 
1.7.10.2