JAL-2704 don't shade gap colour for PID/conservation

[jalview.git] / src / jalview / renderer / ResidueShader.java

diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java
index 7e4f211..aa84816 100644 (file)
--- 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;
   }