JAL-3855 JAL-4124 test checks asymmetric matrices are stored and restored correctly

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

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 37ef069..6518693 100644 (file)
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -114,6 +114,8 @@ 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);
   }
@@ -1561,7 +1563,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       {
         paevals[i][j] = ((i - j < 2)
                 || ((i > 1 && i < 5) && (j > 1 && i < 5))) ? 1 : 0f;
-        paevals[j][i] = paevals[i][j];
+        paevals[j][i] = -paevals[i][j];
       }
     }
     PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
@@ -1571,6 +1573,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
             sq.getLength(), sq.getLength());
     assertEquals(vals[3][4], paevals[3][4]);
+    assertEquals(vals[4][3], paevals[4][3]);
     dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
     Assert.assertNotSame(dummyMat.getNewick(), "");
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
@@ -1602,7 +1605,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
       BitSet newGp = BitSet.valueOf(newlongvals);
       assertTrue(gp.equals(newGp));
     }
-
     File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
             ".jvp");
     new Jalview2XML(false).saveState(tfile);
@@ -1629,7 +1631,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(oldMap.getToRanges(), newMap.getToRanges());
     Assert.assertEquals(oldMap.getFromRatio(), newMap.getFromRatio());
     Assert.assertEquals(oldMap.getToRatio(), newMap.getToRatio());
-
     for (i = sq.getLength() - 1; i >= 0; i--)
     {
       ContactListI oldCM = dummyMat.getContactList(i),
@@ -1645,7 +1646,6 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
     Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
     Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
-
   }
 
 }