- globalColourScheme = ColourSchemeProperty.getColour(alignment,\r
- applet.getParameter("defaultColour"));\r
- if (globalColourScheme != null)\r
+ String colour = applet.getParameter("defaultColour");\r
+\r
+ if(colour == null)\r
+ {\r
+ colour = applet.getParameter("userDefinedColour");\r
+ if(colour !=null)\r
+ colour = "User Defined";\r
+ }\r
+\r
+ if(colour != null)\r
+ {\r
+ globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);\r
+ if (globalColourScheme != null)\r
+ {\r
+ globalColourScheme.setConsensus(vconsensus);\r
+ }\r
+ }\r
+\r
+ if(applet.getParameter("userDefinedColour")!=null)\r