From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 23 Jan 2024 13:39:04 +0000 (+0000)
Subject: Merge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executa... 
X-Git-Tag: Release_2_11_3_3~7^2~6
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=3dcec29e9be7607122fb981050ff2198cef2a746;hp=fc3c0910b7086411d72104c0a2cf4b8b45a95015;p=jalview.git

Merge branch 'bug/JAL-4373_jvmmemmax_and_jvmmempc_ignored_on_command_line_for_executable_jar_launch' into develop
---

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index e01d40a..c848908 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -328,9 +328,17 @@ public class Commands
           }
 
           // colour alignment
-          String colour = avm.getFromSubValArgOrPref(av, Arg.COLOUR, sv,
-                  null, "DEFAULT_COLOUR_PROT", "");
-          this.colourAlignFrame(af, colour);
+          String colour = null;
+          if (avm.containsArg(Arg.COLOUR)
+                  || !(format == FileFormat.Jalview))
+          {
+            colour = avm.getFromSubValArgOrPref(av, Arg.COLOUR, sv, null,
+                    "DEFAULT_COLOUR_PROT", null);
+          }
+          if (colour != null)
+          {
+            this.colourAlignFrame(af, colour);
+          }
 
           // Change alignment frame title
           String title = avm.getFromSubValArgOrPref(av, Arg.TITLE, sv, null,