JAL-2349 add dummy contact for both applet and application

diff --git a/src/jalview/io/AppletFormatAdapter.java b/src/jalview/io/AppletFormatAdapter.java
index 45d65d6..93ff448 100755 (executable)
--- a/src/jalview/io/AppletFormatAdapter.java
+++ b/src/jalview/io/AppletFormatAdapter.java
@@ -26,6 +26,7 @@ import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.AlignmentView;
+import jalview.datamodel.ContactMatrixTest;
 import jalview.datamodel.PDBEntry.Type;
 import jalview.datamodel.SequenceI;
 import jalview.ext.jmol.JmolParser;
@@ -308,6 +309,8 @@ public class AppletFormatAdapter
 
     alignFile.addGroups(al);
 
+    al.addContactList(new ContactMatrixTest(al.getWidth()));
+
     return al;
   }
 

diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 5febda6..3ad74c7 100755 (executable)
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -28,7 +28,6 @@ import jalview.bin.Cache;
 import jalview.bin.Jalview;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.ColumnSelection;
-import jalview.datamodel.ContactMatrixTest;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
@@ -336,8 +335,6 @@ public class FileLoader implements Runnable
 
         if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
         {
-          al.addContactList(new ContactMatrixTest(al.getWidth()));
-
           // construct and register dataset sequences
           for (SequenceI sq : al.getSequences())
           {