Merge branch 'develop' into Release_2_9_0b1_Branch

[jalview.git] / src / jalview / appletgui / AlignViewport.java

diff --git a/src/jalview/appletgui/AlignViewport.java b/src/jalview/appletgui/AlignViewport.java
index f8355c3..9256cfc 100644 (file)
--- 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");