From: Jim Procter <jprocter@issues.jalview.org>
Date: Thu, 31 May 2018 16:20:31 +0000 (+0100)
Subject: JAL-1958 use the annotation score for the sequence being coloured !
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e966ed9e5fb77a7e698344d4a581c3d7450eaf0e;p=jalview.git

JAL-1958 use the annotation score for the sequence being coloured !
---

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 00744c0..7133f13 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -484,12 +484,12 @@ public class AnnotationColourGradient extends FollowerColourScheme
     if (perLineScore)
     {
       trans = (int) ((1f - range) * midtr);
-      range = (float) ((annotation.score - plmin) / (plmax - aamin));
+      range = (float) ((ann.score - plmin) / (plmax - aamin));
     }
     int dr = (int) (redRange * range + redMin),
             dg = (int) (greenRange * range + greenMin),
             db = (int) (blueRange * range + blueMin);
-    if (annotation.score == annotation.score && positionToTransparency)
+    if (ann.score == ann.score && positionToTransparency)
     {
       return new Color(Math.min(dr + trans, midtr), Math.min(dg
               + trans, midtr), Math.min(db + trans, midtr));