JAL-3285 code changes to AnnotationLabels not included in the merge

diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 8aac7dc..bf3ecf2 100755 (executable)
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -366,9 +366,9 @@ public class AnnotationLabels extends JPanel
     // JAL-1264 hide all sequence-specific annotations of this type
     if (selectedRow < aa.length)
     {
-      if (isSequenceAnnotation)
+      if (aa[selectedRow].sequenceRef != null)
       {
-        final String label = ann.label;
+        final String label = aa[selectedRow].label;
         JMenuItem hideType = new JMenuItem();
         String text = MessageManager.getString("label.hide_all") + " "
                 + label;
@@ -403,17 +403,17 @@ public class AnnotationLabels extends JPanel
     // property methods
     if (selectedRow < aa.length)
     {
-      final String label = ann.label;
-      if (!(ann.autoCalculated)
+      final String label = aa[selectedRow].label;
+      if (!(aa[selectedRow].autoCalculated)
               && !(InformationThread.HMM_CALC_ID.equals(ann.getCalcId())))
       {
-        if (ann.graph == AlignmentAnnotation.NO_GRAPH)
+        if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
         {
           // display formatting settings for this row.
           pop.addSeparator();
           // av and sequencegroup need to implement same interface for
           item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
-                  ann.scaleColLabel);
+                         aa[selectedRow].scaleColLabel);
           item.addActionListener(this);
           pop.add(item);
         }