JAL-4160 --colour can now take user defined scheme names and colour scheme-spec defin...

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

diff --git a/src/jalview/bin/Commands.java b/src/jalview/bin/Commands.java
index fc8a51a..64c1e72 100644 (file)
--- 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);
           }