X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=af52edad5c3f42dd974ce358195f19d29c62317d;hb=b3fb6325a8bc315c5c938faf10ffd2e73d965f16;hp=0ab9dcbb565b7a19d16d9c7bc9aa1065bbaa6d58;hpb=a81e74154d35e10958b58c3c9411aa9ee21880a6;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 0ab9dcb..af52eda 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -110,6 +110,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
   @BeforeClass(alwaysRun = true)
   public void setUpJvOptionPane()
   {
+    if (Desktop.instance != null)
+      Desktop.instance.closeAll_actionPerformed(null);
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
@@ -1564,10 +1566,13 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     }
     PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
     String content = ContactMatrix.contactToFloatString(dummyMat);
-    Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
-    float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
-    assertEquals(vals[3][4],paevals[3][4]);
+    Assert.assertTrue(content.contains("\t1.")); // at least one element must be
+                                                 // 1
+    float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
+            sq.getLength(), sq.getLength());
+    assertEquals(vals[3][4], paevals[3][4]);
     dummyMat.makeGroups(0.5f, false);
+    Assert.assertNotSame(dummyMat.getNewick(), "");
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);
     File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
@@ -1598,12 +1603,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
         Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
       }
     }
-    Assert.assertEquals(dummyMat.hasGroups(), restoredMat.hasGroups());
-    Assert.assertEquals(dummyMat.getGroups(), restoredMat.getGroups());
-    Assert.assertEquals(dummyMat.hasTree(), restoredMat.hasTree());
-    Assert.assertEquals(dummyMat.getNewick(), restoredMat.getNewick());
-    
-    
+    Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
+    Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
+    Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
+    Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
   }
 
 }