JAL-2624 check feature colour threshold when colouring structure

[jalview.git] / src / jalview / appletgui / FeatureColourChooser.java

diff --git a/src/jalview/appletgui/FeatureColourChooser.java b/src/jalview/appletgui/FeatureColourChooser.java
index 3dc69e6..4075e8b 100644 (file)
--- a/src/jalview/appletgui/FeatureColourChooser.java
+++ b/src/jalview/appletgui/FeatureColourChooser.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -95,9 +95,11 @@ public class FeatureColourChooser extends Panel implements ActionListener,
     float mm[] = fr.getMinMax().get(type)[0];
     min = mm[0];
     max = mm[1];
+    threshline = new GraphLine((max - min) / 2f, "Threshold", Color.black);
     oldcs = fr.getFeatureColours().get(type);
     if (oldcs.isGraduatedColour())
     {
+      threshline.value = oldcs.getThreshold();
       cs = new FeatureColour((FeatureColour) oldcs, min, max);
     }
     else
@@ -384,14 +386,6 @@ public class FeatureColourChooser extends Panel implements ActionListener,
       thresholdValue.setText("");
     }
 
-    else if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD
-            && threshline == null)
-    {
-      // todo visual indication of feature threshold
-      threshline = new jalview.datamodel.GraphLine((max - min) / 2f,
-              "Threshold", Color.black);
-    }
-
     if (aboveThreshold != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;