From: j.procter@dundee.ac.uk <jprocter@jims-mbp-2.dyn.lifesci.dundee.ac.uk>
Date: Fri, 18 Jul 2014 12:32:23 +0000 (+0100)
Subject: JAL-795 take colour from annotation if colour is present
X-Git-Tag: Jalview_2_9~179^2~6
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=862f76c4b933814aba67bc132c586811680d3ef5

JAL-795 take colour from annotation if colour is present
---

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)