X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=a89d7ced02d5a9f4dd868916390834739f5af11f;hb=7d722306ebba9a2d6562849c598a91d867f7d00e;hp=36825eaf99f612a03aad300f068eff66629c263c;hpb=7abcbfb6619828a810ed1a9dddd870f70bf8bcd1;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 36825ea..a89d7ce 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -140,8 +140,15 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     if (shader.getColourScheme() != null)
     {
-      resBoxColour = shader.findColour(seq.getCharAt(i),
+      if (forOverview && Comparison.isGap(seq.getCharAt(i)))
+      {
+        resBoxColour = Color.lightGray;
+      }
+      else
+      {
+        resBoxColour = shader.findColour(seq.getCharAt(i),
               i, seq);
+      }
     }
     else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
     {