JAL-629 Tidy up tests and replaced methods before merge to develop

[jalview.git] / test / jalview / project / Jalview2xmlTests.java

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 81756e0..af52eda 100644 (file)
--- 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);
   }
@@ -1564,9 +1566,11 @@ 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);
@@ -1602,9 +1606,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
     Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
     Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
-    Assert.assertEquals( restoredMat.getNewick(),dummyMat.getNewick());
-    
-    
+    Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
   }
 
 }