JAL-2588 Gap colour scheme now shown in overview

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

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 51b1a3a..7a1e263 100755 (executable)
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -140,7 +140,8 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
   {
     if (shader.getColourScheme() != null)
     {
-      if (forOverview && Comparison.isGap(seq.getCharAt(i)))
+      if (forOverview && Comparison.isGap(seq.getCharAt(i))
+              && !shader.getColourScheme().hasGapColour())
       {
         resBoxColour = Color.lightGray;
       }