X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=1f86d870cf4da4c6c354963d1cb35a48cb088f84;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;hp=3c552a412dace3dabb1e438ce32c4e63c66f5a6f;hpb=8ba93f7655ea7165579539158b6a5eb076135bba;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 3c552a4..1f86d87 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -22,6 +22,7 @@ package jalview.gui;
 
 import jalview.bin.Cache;
 import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
 import jalview.datamodel.SequenceGroup;
 import jalview.schemes.AnnotationColourGradient;
 import jalview.schemes.ColourSchemeI;
@@ -724,9 +725,19 @@ public class AnnotationColourChooser extends JPanel
     for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
     {
       AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[i];
-      if (aa.label.equals(currentAnnotation.label))
+      if (aa.label.equals(currentAnnotation.label)
+              && (currentAnnotation.getCalcId() == null ? aa.getCalcId() == null
+                      : currentAnnotation.getCalcId()
+                              .equals(aa.getCalcId())))
       {
-        aa.threshold.value = thr;
+        if (aa.threshold == null)
+        {
+          aa.threshold = new GraphLine(currentAnnotation.threshold);
+        }
+        else
+        {
+          aa.threshold.value = thr;
+        }
       }
     }
   }