X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbin%2FCommands.java;fp=src%2Fjalview%2Fbin%2FCommands.java;h=64c1e7292a9f996ceeddccd9e341f7e9e02b4c8d;hb=55be75760a07698418e5c5cf4d84119f19a5ba4d;hp=fc8a51a4933f22599a1b61a9702140eaa820a56b;hpb=340ebd50b63087b4f8b2c4a26d94112dc51ada9c;p=jalview.git

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index fc8a51a..64c1e72 100644
--- a/src/jalview/bin/Commands.java
+++ b/src/jalview/bin/Commands.java
@@ -44,6 +44,8 @@ import jalview.io.FileLoader;
 import jalview.io.HtmlSvgOutput;
 import jalview.io.IdentifyFile;
 import jalview.io.NewickFile;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
 import jalview.structure.StructureImportSettings.TFType;
 import jalview.structure.StructureSelectionManager;
 import jalview.util.FileUtils;
@@ -259,7 +261,15 @@ public class Commands
                   Arg.COLOUR, sv, null, "DEFAULT_COLOUR_PROT", "");
           if ("" != colour)
           {
-            af.changeColour_actionPerformed(colour);
+            ColourSchemeI cs = ColourSchemeProperty.getColourScheme(
+                    af.getViewport(), af.getViewport().getAlignment(), colour);
+            
+            if (cs==null && !"None".equals(colour))
+            {
+              Console.warn("Couldn't parse '"+colour+"' as a colourscheme.");
+            } else {
+              af.changeColour(cs);
+            }
             Jalview.testoutput(argParser, Arg.COLOUR, "zappo", colour);
           }