Merge branch 'bug/JAL-4368_default_colourscheme_applied_to_JVP_inappropriately' into...

[jalview.git] / src / jalview / bin / Commands.java

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index e01d40a..c848908 100644 (file)
--- 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,