JAL-2346 restore choice of annotation for colouring faithfully

[jalview.git] / src / jalview / gui / AnnotationColourChooser.java

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 39cde03..4daf6b2 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -20,12 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.bin.Cache;
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Dimension;
@@ -35,6 +29,13 @@ import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.util.Hashtable;
+import java.util.Vector;
+
+import jalview.bin.Cache;
+import jalview.datamodel.SequenceGroup;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
 
 import javax.swing.BorderFactory;
 import javax.swing.JButton;
@@ -118,15 +119,17 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       seqAssociated.setSelected(acg.isSeqAssociated());
 
     }
-    annotations = new JComboBox<String>(
-            getAnnotationItems(seqAssociated.isSelected()));
+    Vector<String> annotItems = getAnnotationItems(seqAssociated
+            .isSelected());
+    annotations = new JComboBox<String>(annotItems);
 
     populateThresholdComboBox(threshold);
 
     if (oldcs instanceof AnnotationColourGradient)
     {
       AnnotationColourGradient acg = (AnnotationColourGradient) oldcs;
-      annotations.setSelectedItem(acg.getAnnotation());
+      String label = getAnnotationMenuLabel(acg.getAnnotation());
+      annotations.setSelectedItem(label);
       switch (acg.getAboveThreshold())
       {
       case AnnotationColourGradient.NO_THRESHOLD:
@@ -143,7 +146,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
                 MessageManager
                         .getString("error.implementation_error_dont_know_about_threshold_setting"));
       }
-      thresholdIsMin.setSelected(acg.thresholdIsMinMax);
+      thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
       thresholdValue.setText("" + acg.getAnnotationThreshold());
     }
 
@@ -475,7 +478,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       thresholdValue.setEnabled(true);
       adjusting = false;
     }
-    colorAlignmContaining(getCurrentAnnotation(), selectedThresholdItem);
+    colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
 
     ap.alignmentChanged();
     // ensure all associated views (overviews, structures, etc) are notified of