From 69827911885f6e7ed824b5e6f2f802e0a23c25f0 Mon Sep 17 00:00:00 2001 From: Ben Soares Date: Fri, 5 Jan 2024 17:28:36 +0000 Subject: [PATCH 1/1] JAL-4368 Only set a colour scheme if --colour is given or it's not a JVP file --- src/jalview/bin/Commands.java | 14 +++++++++++--- 1 file changed, 11 insertions(+), 3 deletions(-) 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, -- 1.7.10.2