X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSequenceRenderer.java;h=86d1f98e51ec53f834954274fc85672769b8150d;hb=4f094851cd2247ea2d982e7829a6f5b663042573;hp=1c7c4ce85c32ad89ab7b32d6d2f562078a88a437;hpb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;p=jalview.git

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 1c7c4ce..86d1f98 100755
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -83,7 +83,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
     }
     else if (av.getShowBoxes())
     {
-      getBoxColour(av.getViewportColourScheme(), seq, i);
+      getBoxColour(av.getResidueShading(), seq, i);
     }
 
     return resBoxColour;
@@ -182,7 +182,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
         }
         else if (av.getShowBoxes())
         {
-          getBoxColour(av.getViewportColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
         }
       }
 
@@ -272,7 +272,7 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
 
         if (av.getColourText())
         {
-          getBoxColour(av.getViewportColourScheme(), seq, i);
+          getBoxColour(av.getResidueShading(), seq, i);
           if (av.getShowBoxes())
           {
             graphics.setColor(resBoxColour.darker());