X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FResidueShader.java;fp=src%2Fjalview%2Frenderer%2FResidueShader.java;h=aa84816a83108d0c89aa859acd7ae8e3a214c944;hb=991d2210e8e086bde29a90bdf21979261442d889;hp=7e4f2118cec87c0ce7ecb73c9d49a4f3a75c9296;hpb=806c9dc4a3d841fe36e7d17ab45d783a9fc95f26;p=jalview.git

diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java
index 7e4f211..aa84816 100644
--- a/src/jalview/renderer/ResidueShader.java
+++ b/src/jalview/renderer/ResidueShader.java
@@ -250,7 +250,10 @@ public class ResidueShader implements ResidueShaderI
     /*
      * apply PID threshold and consensus fading if in force
      */
-    colour = adjustColour(symbol, position, colour);
+    if (!Comparison.isGap(symbol))
+    {
+      colour = adjustColour(symbol, position, colour);
+    }
 
     return colour;
   }