X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;fp=test%2Fjalview%2Fproject%2FJalview2xmlTests.java;h=c9532cc058fdf4d88290e30dcc8214ef4b0ed3ef;hb=cfd38a33612b73a5b050c9f19d0fb0d81a7b646a;hp=37f946b95e9295e245dfda69d562627e51f415bc;hpb=de9592c0781569ccefd4c115bb36524d6c9deaab;p=jalview.git

diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 37f946b..c9532cc 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -1563,7 +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);
@@ -1573,7 +1573,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
             sq.getLength(), sq.getLength());
     assertEquals(vals[3][4], paevals[3][4]);
-    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
+    assertEquals(vals[4][3], paevals[4][3]);
+    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, false,0.5f, false));
     Assert.assertNotSame(dummyMat.getNewick(), "");
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);