From 9483294f728bf319f90322fbe4dd5aacc6e9fa45 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Fri, 2 Dec 2016 14:02:09 +0000
Subject: [PATCH] JAL-2346 fixed bug (in code not reached by Jalview)

---
 src/jalview/schemes/AnnotationColourGradient.java |   34 +++++++++++++--------
 1 file changed, 21 insertions(+), 13 deletions(-)

diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index 2c8d5dd..856bee9 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -289,8 +289,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
     }
     if ((threshold == 0) || aboveThreshold(c, j))
     {
-      if (ann.annotations != null
-              && j < ann.annotations.length
+      if (ann.annotations != null && j < ann.annotations.length
               && ann.annotations[j] != null
               && !jalview.util.Comparison.isGap(c))
       {
@@ -372,31 +371,41 @@ public class AnnotationColourGradient extends FollowerColourScheme
     return currentColour;
   }
 
-  private Color shadeCalculation(AlignmentAnnotation ann, int j)
+  /**
+   * Returns a graduated colour for the annotation at the given column. If there
+   * is a threshold value, and it is used as the top/bottom of the colour range,
+   * and the value satisfies the threshold condition, then a colour
+   * proportionate to the range from the threshold is calculated. For all other
+   * cases, a colour proportionate to the annotation's min-max range is
+   * calulated. Note that thresholding is _not_ done here (a colour is computed
+   * even if threshold is not passed), but by the renderer.
+   * 
+   * @param ann
+   * @param col
+   * @return
+   */
+  Color shadeCalculation(AlignmentAnnotation ann, int col)
   {
-
-    // calculate a shade
     float range = 1f;
+    float value = ann.annotations[col].value;
     if (thresholdIsMinMax && ann.threshold != null
             && aboveAnnotationThreshold == ABOVE_THRESHOLD
-            && ann.annotations[j].value >= ann.threshold.value)
+            && value >= ann.threshold.value)
     {
-      range = (ann.annotations[j].value - ann.threshold.value)
+      range = (value - ann.threshold.value)
               / (ann.graphMax - ann.threshold.value);
     }
     else if (thresholdIsMinMax && ann.threshold != null
             && aboveAnnotationThreshold == BELOW_THRESHOLD
-            && ann.annotations[j].value >= ann.graphMin)
+            && value <= ann.threshold.value)
     {
-      range = (ann.annotations[j].value - ann.graphMin)
-              / (ann.threshold.value - ann.graphMin);
+      range = (value - ann.graphMin) / (ann.threshold.value - ann.graphMin);
     }
     else
     {
       if (ann.graphMax != ann.graphMin)
       {
-        range = (ann.annotations[j].value - ann.graphMin)
-                / (ann.graphMax - ann.graphMin);
+        range = (value - ann.graphMin) / (ann.graphMax - ann.graphMin);
       }
       else
       {
@@ -409,7 +418,6 @@ public class AnnotationColourGradient extends FollowerColourScheme
     int db = (int) (blueRange * range + blueMin);
 
     return new Color(dr, dg, db);
-
   }
 
   public boolean isPredefinedColours()
-- 
1.7.10.2