X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAnnotationColumnChooser.java;h=b9595e7f00270ddf012340d36e9d7b115ecd7874;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=b342a83dcd6e288f83ae56a291938e90df43ab2a;hpb=a90e2fe3cc3b779521a81cf8de410936f3a777c1;p=jalview.git

diff --git a/src/jalview/appletgui/AnnotationColumnChooser.java b/src/jalview/appletgui/AnnotationColumnChooser.java
index b342a83..b9595e7 100644
--- a/src/jalview/appletgui/AnnotationColumnChooser.java
+++ b/src/jalview/appletgui/AnnotationColumnChooser.java
@@ -135,17 +135,22 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     slider.addAdjustmentListener(this);
     slider.addMouseListener(this);
 
-    if (av.getAlignment().getAlignmentAnnotation() == null)
+    AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation();
+    if (anns == null)
     {
       return;
     }
     setOldColumnSelection(av.getColumnSelection());
     adjusting = true;
-    Vector list = new Vector();
+    Vector<String> list = new Vector<String>();
     int index = 1;
-    for (int i = 0; i < av.getAlignment().getAlignmentAnnotation().length; i++)
+    for (int i = 0; i < anns.length; i++)
     {
-      String label = av.getAlignment().getAlignmentAnnotation()[i].label;
+      String label = anns[i].label;
+      if (anns[i].sequenceRef != null)
+      {
+        label = label + "_" + anns[i].sequenceRef.getName();
+      }
       if (!list.contains(label))
       {
         list.addElement(label);
@@ -273,6 +278,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     this.validate();
   }
 
+  @Override
   @SuppressWarnings("unchecked")
   public void reset()
   {
@@ -302,6 +308,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
 
   }
 
+  @Override
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     if (!adjusting)
@@ -343,6 +350,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     });
   }
 
+  @Override
   public void valueChanged(boolean updateAllAnnotation)
   {
     if (slider.isEnabled())
@@ -866,6 +874,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter implements
     }
   }
 
+  @Override
   public void actionPerformed(ActionEvent evt)
   {
     if (evt.getSource() == thresholdValue)