Merge branch 'releases/Release_2_10_3_Branch'

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

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 676d3cf..ef87671 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1603,10 +1603,12 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       System.exit(0);
     }
-    else
+
+    viewport = null;
+    if (alignPanel != null && alignPanel.overviewPanel != null)
     {
+      alignPanel.overviewPanel.dispose();
     }
-    viewport = null;
     alignPanel = null;
     this.dispose();
   }
@@ -4147,7 +4149,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       // register the association(s) and quit, don't create any windows.
       if (StructureSelectionManager.getStructureSelectionManager(applet)
-              .setMapping(seqs, chains, pdb.getFile(), protocol) == null)
+              .setMapping(seqs, chains, pdb.getFile(), protocol, null) == null)
       {
         System.err.println("Failed to map " + pdb.getFile() + " ("
                 + protocol + ") to any sequences");