X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=92e24bf8f335e9ad23b4c81d053a53d539138d69;hb=15a31f818e6ee79cb23ac4acd09575ab36cdb2ae;hp=96e61e9f1a34bc4e6f57601f2e23332fec791a41;hpb=d423f22792e47dbc800ae220a58677f988971d06;p=jalview.git

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 96e61e9..92e24bf 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -1440,7 +1440,7 @@ public class PopupMenu extends JPopupMenu
     SequenceGroup sg = getGroup();
     EditNameDialog dialog = new EditNameDialog(sg.getName(), sg
             .getDescription(), "       Group Name ", "Group Description ",
-            "Edit Group Name/Description");
+            "Edit Group Name/Description",ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1479,7 +1479,7 @@ public class PopupMenu extends JPopupMenu
   {
     EditNameDialog dialog = new EditNameDialog(sequence.getName(), sequence
             .getDescription(), "       Sequence Name ",
-            "Sequence Description ", "Edit Sequence Name/Description");
+            "Sequence Description ", "Edit Sequence Name/Description",ap.alignFrame);
 
     if (!dialog.accept)
     {
@@ -1698,10 +1698,12 @@ public class PopupMenu extends JPopupMenu
     omitHidden = ap.av.getViewAsString(true);
     Alignment oal = new Alignment(ap.av.getSequenceSelection());
     AlignmentAnnotation[] nala = ap.av.alignment.getAlignmentAnnotation();
-    for (int i = 0; i < nala.length; i++)
-    {
-      AlignmentAnnotation na = nala[i];
-      oal.addAnnotation(na);
+    if (nala!=null) {
+      for (int i = 0; i < nala.length; i++)
+      {
+        AlignmentAnnotation na = nala[i];
+        oal.addAnnotation(na);
+      }
     }
     cap.setText(new FormatAdapter().formatSequences(e.getActionCommand(),
             oal, omitHidden, csel, sg));
@@ -1868,7 +1870,7 @@ public class PopupMenu extends JPopupMenu
 
       EditNameDialog dialog = new EditNameDialog(sequence
               .getSequenceAsString(sg.getStartRes(), sg.getEndRes() + 1),
-              null, "Edit Sequence ", null, "Edit Sequence");
+              null, "Edit Sequence ", null, "Edit Sequence",ap.alignFrame);
 
       if (dialog.accept)
       {