X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignViewport.java;h=7ef2d59c3fd8c0eb6a7d041578400a2ad05eb0c7;hb=ce2fafc54fbec56f100776d81e26fa146ee7d7a1;hp=e434825a8e94f029d272696b1174b35d3120ae3b;hpb=47df71b2e12f6503e956705c9c9d9a7c14b5bd14;p=jalview.git

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index e434825..7ef2d59 100644
--- a/src/jalview/appletgui/AlignViewport.java
+++ b/src/jalview/appletgui/AlignViewport.java
@@ -187,8 +187,13 @@ public class AlignViewport extends AlignmentViewport implements
 
     if (applet != null)
     {
-      String colour = applet.getParameter("defaultColour");
-
+      String colour = al.isNucleotide() ? applet
+              .getParameter("defaultColourNuc") : applet
+              .getParameter("defaultColourProt");
+      if (colour == null)
+      {
+        colour = applet.getParameter("defaultColour");
+      }
       if (colour == null)
       {
         colour = applet.getParameter("userDefinedColour");