JAL-2588 Check/fix show boxes settings + unit test updates.

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

diff --git a/src/jalview/appletgui/SequenceRenderer.java b/src/jalview/appletgui/SequenceRenderer.java
index 516dcc1..684701e 100755 (executable)
--- a/src/jalview/appletgui/SequenceRenderer.java
+++ b/src/jalview/appletgui/SequenceRenderer.java
@@ -84,7 +84,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     // TODO replace 8 or so code duplications with calls to this method
     // (refactored as needed)
-    return resColourFinder.getResidueColour(av.getResidueShading(),
+    return resColourFinder.getResidueColour(av.getShowBoxes(),
+            av.getResidueShading(),
             allGroups, seq, position, finder);
   }