From: James Procter <j.procter@dundee.ac.uk>
Date: Tue, 23 Jan 2024 13:34:35 +0000 (+0000)
Subject: Merge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into... 
X-Git-Tag: Release_2_11_3_3~7^2~7
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=cc58c69c02ae426819761564b54161d05e6f94e9;hp=546cce1523d08c53ffdc744d46907cf8c98bdc10;p=jalview.git

Merge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' 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,