X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FAnnotationColourGradient.java;h=e975884e6fcaaf6fab9116c90827e6398310c7af;hb=862f76c4b933814aba67bc132c586811680d3ef5;hp=f467cb8c108777d95ace28bd4ca5fdebabc08e12;hpb=25bf7406cdf030f4b5d87d3e93d0fd769d956b19;p=jalview.git

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index f467cb8..e975884 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -233,14 +233,20 @@ public class AnnotationColourGradient extends FollowerColourScheme
               && !jalview.util.Comparison.isGap(c))
       {
 
-        if (predefinedColours)
+        if (annotation.annotations[j].colour != null)
         {
-          if (annotation.annotations[j].colour != null)
+          if (predefinedColours || annotation.hasIcons)
+          {
             return annotation.annotations[j].colour;
-          else
+          }
+        }
+        else
+        {
+          if (predefinedColours)
+          {
             return currentColour;
+          }
         }
-
         if (aboveAnnotationThreshold == NO_THRESHOLD
                 || (annotationThreshold != null
                         && aboveAnnotationThreshold == ABOVE_THRESHOLD && annotation.annotations[j].value >= annotationThreshold.value)