Colour argument added, to mirror applet view

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 50faf67..e5ad207 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -164,6 +164,28 @@ public class Jalview
 \r
             AlignFrame af = fileLoader.LoadFileWaitTillLoaded(file, protocol, format);\r
 \r
+            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
@@ -228,9 +250,11 @@ public class Jalview
           }\r
 \r
         // We'll only open the default file if the desktop is visible.\r
+        // And the user\r
         //////////////////////\r
           if (\r
               !headless\r
+          && file==null\r
           && jalview.bin.Cache.getDefault("SHOW_STARTUP_FILE", true)\r
                     )\r
           {\r