JAL-621 and JAL-564

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 2e9b7ea..1997264 100755 (executable)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -30,6 +30,7 @@ import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
 
 public class AlignFrame extends EmbmenuFrame implements ActionListener,
         ItemListener, KeyListener
@@ -139,6 +140,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     alignPanel.idPanel.idCanvas.addKeyListener(this);
     alignPanel.scalePanel.addKeyListener(this);
     alignPanel.annotationPanel.addKeyListener(this);
+    alignPanel.annotationPanelHolder.addKeyListener(this);
+    alignPanel.annotationSpaceFillerHolder.addKeyListener(this);
+    alignPanel.alabels.addKeyListener(this);
     createAlignFrameWindow(embedded, title);
     alignPanel.validate();
     alignPanel.paintAlignment(true);
@@ -3489,6 +3493,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
         return;
       }
     }
+    if (applet.useXtrnalSviewer)
+    {
+      // register the association(s) and quit, don't create any windows.
+      StructureSelectionManager.getStructureSelectionManager().setMapping(seqs, chains, pdb.getFile(), protocol);
+      return;
+    }
     if (applet.isAlignPdbStructures() && applet.jmolAvailable)
     {
       // can only do alignments with Jmol