JAL-2588 Naive implementation of gaps as grey in overview

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 36825ea..a89d7ce 100755 (executable)
--- 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)))
     {