From: Jim Procter <jprocter@issues.jalview.org>
Date: Sun, 4 Dec 2016 12:22:23 +0000 (+0000)
Subject: JAL-2349 add dummy contact for both applet and application
X-Git-Tag: Release_2_11_3_0~23^2~60^2~9^2~26
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=a81d5dedad0d679f576a7c0f165d99dbc6cdb63b;p=jalview.git

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
--- 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
--- 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())
           {