JAL-795 hack to ignore black colour in annotation element.

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 3cada8b..efad430 100755 (executable)
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -286,7 +286,8 @@ public class AnnotationColourGradient extends FollowerColourScheme
                 || (annotationThreshold != null && (aboveAnnotationThreshold == ABOVE_THRESHOLD ? aj.value >= annotationThreshold.value
                         : aj.value <= annotationThreshold.value)))
         {
-          if (predefinedColours && aj.colour != null)
+          if (predefinedColours && aj.colour != null
+                  && !aj.colour.equals(Color.black))
           {
             currentColour = aj.colour;
           }