X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=ea857cbcda7c7b6bb4662218ca5ab5ae09836804;hb=6d6d6bc08bca95676a8175c634c03c163fb88684;hp=a13b64321b715604f74e220f1734dc57c4a3595b;hpb=4c61bddcb9e367db694e3f2bde9c4d25f114f50b;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index a13b643..ea857cb 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -66,6 +66,8 @@ public class SequenceRenderer
       {
         if( currentSequenceGroup.getDisplayBoxes())
              getBoxColour(currentSequenceGroup.cs, seq, i);
+        else
+             resBoxColour = Color.white;
       }
       else if(av.getShowBoxes())
             getBoxColour(av.getGlobalColourScheme(), seq, i);
@@ -101,7 +103,6 @@ public class SequenceRenderer
     char s;
     // Need to find the sequence position here.
 
-    graphics.setColor(Color.black);
     String sequence  = seq.getSequence();
     for (int i = start; i <= end; i++)
     {
@@ -138,6 +139,8 @@ public class SequenceRenderer
             else
               graphics.setColor(resBoxColour);
            }
+           else
+             graphics.setColor(Color.black);
         }
 
           charOffset =  (width - fm.charWidth(s))/2;