X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=1bc1b515bc8439254bf29b060e768141784996f8;hb=54b44faea7413a39963c535fa728b6e415dfe989;hp=481a657501204114037cf42065ec41e75555c0a7;hpb=245ddd4612033edc65de15acb93ac9c22912a828;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index 481a657..1bc1b51 100755
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -56,7 +56,7 @@ public class AlignViewport
   boolean conservationColourSelected = false;
   boolean abovePIDThreshold = false;
 
-  SequenceGroup selectionGroup = new SequenceGroup();
+  SequenceGroup selectionGroup;
 
   int charHeight;
   int charWidth;
@@ -79,7 +79,7 @@ public class AlignViewport
 
   // The following vector holds the features which are
  // currently visible, in the correct order or rendering
-  Hashtable featuresDisplayed = null;
+  Hashtable featuresDisplayed;
 
 
   public Vector vconsensus;
@@ -141,14 +141,34 @@ public class AlignViewport
     updateConservation();
     updateConsensus();
 
-    if (applet != null && applet.getParameter("defaultColour") != null)
+
+    if (applet != null)
     {
-      globalColourScheme = ColourSchemeProperty.getColour(alignment,
-          applet.getParameter("defaultColour"));
-      if (globalColourScheme != null)
+      String colour = applet.getParameter("defaultColour");
+
+      if(colour == null)
+      {
+        colour = applet.getParameter("userDefinedColour");
+        if(colour !=null)
+          colour = "User Defined";
+      }
+
+      if(colour != null)
+      {
+        globalColourScheme = ColourSchemeProperty.getColour(alignment, colour);
+        if (globalColourScheme != null)
+        {
+          globalColourScheme.setConsensus(vconsensus);
+        }
+      }
+
+      if(applet.getParameter("userDefinedColour")!=null)
       {
-        globalColourScheme.setConsensus(vconsensus);
+        ((UserColourScheme)globalColourScheme).parseAppletParameter(
+            applet.getParameter("userDefinedColour"));
       }
+
+
     }
   }