JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/appletgui/AnnotationLabels.java b/src/jalview/appletgui/AnnotationLabels.java
index d8e7007..1366f31 100755 (executable)
--- a/src/jalview/appletgui/AnnotationLabels.java
+++ b/src/jalview/appletgui/AnnotationLabels.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 import jalview.analysis.AlignmentUtils;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.util.MessageManager;
@@ -51,7 +52,6 @@ import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
 import java.util.Arrays;
 import java.util.Collections;
-import java.util.Vector;
 
 public class AnnotationLabels extends Panel
         implements ActionListener, MouseListener, MouseMotionListener
@@ -202,7 +202,9 @@ public class AnnotationLabels extends Panel
     }
     else if (evt.getActionCommand().equals(COPYCONS_SEQ))
     {
-      SequenceI cons = av.getConsensusSeq();
+      SequenceGroup group = aa[selectedRow].groupRef;
+      SequenceI cons = group == null ? av.getConsensusSeq()
+              : group.getConsensusSeq();
       if (cons != null)
       {
         copy_annotseqtoclipboard(cons);
@@ -843,8 +845,8 @@ public class AnnotationLabels extends Panel
                     + "\t" + sq.getSequenceAsString() + "\n");
     if (av.hasHiddenColumns())
     {
-      jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector<>(
-              av.getAlignment().getHiddenColumns().getHiddenColumnsCopy());
+      jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns(
+              av.getAlignment().getHiddenColumns());
     }
   }