X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fio%2FCrossRef2xmlTests.java;h=34cc17f07ad04195a95cb17ce5bedc9de92a437e;hb=4bc5c1c97bd08007b2ac9ccfd9b3cb29eac10193;hp=3ca6ed815da471d0d56e0ba1aae904338f54e68e;hpb=006890b02106eb31841e6e84d75f1027434823e0;p=jalview.git

diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 3ca6ed8..34cc17f 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -24,20 +24,6 @@ import static org.testng.Assert.assertEquals;
 import static org.testng.Assert.assertNotNull;
 import static org.testng.Assert.assertTrue;
 
-import jalview.analysis.CrossRef;
-import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignedCodonFrame;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.AlignmentTest;
-import jalview.datamodel.SequenceI;
-import jalview.gui.AlignFrame;
-import jalview.gui.CrossRefAction;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.gui.SequenceFetcher;
-import jalview.project.Jalview2XML;
-import jalview.util.DBRefUtils;
-
 import java.io.File;
 import java.io.IOException;
 import java.util.ArrayList;
@@ -51,6 +37,19 @@ import org.testng.annotations.BeforeClass;
 import org.testng.annotations.DataProvider;
 import org.testng.annotations.Test;
 
+import jalview.analysis.CrossRef;
+import jalview.api.AlignmentViewPanel;
+import jalview.datamodel.AlignedCodonFrame;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.AlignmentTest;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.CrossRefAction;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.gui.SequenceFetcher;
+import jalview.project.Jalview2XML;
+import jalview.util.DBRefUtils;
 import junit.extensions.PA;
 
 @Test(singleThreaded = true)
@@ -187,7 +186,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
         SequenceFetcher sf = new SequenceFetcher(Desktop.instance,
                 forSource, forAccession);
         sf.run();
-        AlignFrame[] afs = Desktop.getAlignFrames();
+        AlignFrame[] afs = Desktop.getDesktopAlignFrames();
         if (afs.length == 0)
         {
           failedDBRetr.add("Didn't retrieve " + first);
@@ -211,7 +210,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
       }
       else
       {
-        Desktop.instance.closeAll_actionPerformed(null);
+        if (Desktop.instance != null)
+          Desktop.instance.closeAll_actionPerformed(null);
         // recover stored project
         af = new FileLoader(false).LoadFileWaitTillLoaded(
                 savedProjects.get(first).toString(), DataSourceType.FILE);
@@ -278,7 +278,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
           }
           else
           {
-            Desktop.instance.closeAll_actionPerformed(null);
+            if (Desktop.instance != null)
+              Desktop.instance.closeAll_actionPerformed(null);
             pass3 = 0;
             // recover stored project
             File storedProject = savedProjects.get(nextxref);
@@ -389,7 +390,8 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                 }
                 else
                 {
-                  Desktop.instance.closeAll_actionPerformed(null);
+                  if (Desktop.instance != null)
+                    Desktop.instance.closeAll_actionPerformed(null);
                   // recover stored project
                   File storedProject = savedProjects.get(nextnextxref);
                   if (storedProject == null)