X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSequenceRenderer.java;h=7a1e26325a626aacdd402542746d13cd41c41604;hb=93661ff97ede19d69fde4e2d15f12a7e8963f084;hp=2a2a0cfeafcd2acf730be6b8e2e16b920089c15f;hpb=3fca8f1a5cebad8b73747d121622d1f63a5f9178;p=jalview.git

diff --git a/src/jalview/gui/SequenceRenderer.java b/src/jalview/gui/SequenceRenderer.java
index 2a2a0cf..7a1e263 100755
--- a/src/jalview/gui/SequenceRenderer.java
+++ b/src/jalview/gui/SequenceRenderer.java
@@ -138,12 +138,20 @@ public class SequenceRenderer implements jalview.api.SequenceRenderer
    */
   void getBoxColour(ResidueShaderI shader, SequenceI seq, int i)
   {
-    if (shader != null)
+    if (shader.getColourScheme() != null)
     {
-      resBoxColour = shader.findColour(seq.getCharAt(i),
+      if (forOverview && Comparison.isGap(seq.getCharAt(i))
+              && !shader.getColourScheme().hasGapColour())
+      {
+        resBoxColour = Color.lightGray;
+      }
+      else
+      {
+        resBoxColour = shader.findColour(seq.getCharAt(i),
               i, seq);
+      }
     }
-    else if (forOverview && !Comparison.isGap(seq.getCharAt(i)))
+    else if (forOverview && Comparison.isGap(seq.getCharAt(i)))
     {
       resBoxColour = Color.lightGray;
     }