From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 14 Feb 2017 14:02:03 +0000 (+0000)
Subject: JAL-2346 remove refactored fields, fix test for above threshold
X-Git-Tag: Release_2_10_3b1~336^2~2^2~1^2~2^2~5
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=0f8b0be8f639688f8b83df5bccc7e9b45293f638;p=jalview.git

JAL-2346 remove refactored fields, fix test for above threshold
---

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index c1dcee7..bc5bc54 100644
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -59,17 +59,9 @@ public abstract class AnnotationRowFilter extends JPanel
   protected int[] annmap;
 
   protected boolean adjusting = false;
-  
-  protected JCheckBox currentColours = new JCheckBox();
-
-  protected JPanel minColour = new JPanel();
-
-  protected JPanel maxColour = new JPanel();
 
   protected JCheckBox seqAssociated = new JCheckBox();
 
-  protected JCheckBox thresholdIsMin = new JCheckBox();
-
   protected JSlider slider = new JSlider();
 
   protected JTextField thresholdValue = new JTextField(20);
diff --git a/src/jalview/schemes/AnnotationColourGradient.java b/src/jalview/schemes/AnnotationColourGradient.java
index a5d779d..220d3ab 100755
--- a/src/jalview/schemes/AnnotationColourGradient.java
+++ b/src/jalview/schemes/AnnotationColourGradient.java
@@ -316,7 +316,7 @@ public class AnnotationColourGradient extends FollowerColourScheme
      */
     if (annotationThreshold != null)
     {
-      if ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value >= annotationThreshold.value)
+      if ((aboveAnnotationThreshold == ABOVE_THRESHOLD && aj.value < annotationThreshold.value)
               || (aboveAnnotationThreshold == BELOW_THRESHOLD && aj.value > annotationThreshold.value))
       {
         return Color.white;