+ data = aparser.getValue("colour");\r
+ if(data!=null)\r
+ {\r
+ data.replaceAll("%20", " ");\r
+\r
+ jalview.schemes.ColourSchemeI cs =\r
+ jalview.schemes.ColourSchemeProperty.getColour(af.getViewport().\r
+ getAlignment(), data);\r
+\r
+ if(cs == null)\r
+ {\r
+ jalview.schemes.UserColourScheme ucs\r
+ = new jalview.schemes.UserColourScheme("white");\r
+ ucs.parseAppletParameter(data);\r
+ cs = ucs;\r
+ }\r
+\r
+ System.out.println("colour is " + data);\r
+ af.changeColour( cs );\r
+ }\r
+\r
+\r
+ // Must maintain ability to use the groups flag\r
+ data = aparser.getValue("groups");\r
+ if (data != null)\r