X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=test%2Fjalview%2Fdatamodel%2FPAEContactMatrixTest.java;h=fa7aca5882a325a696b04732f8d70b72cc50e504;hb=33e1f07ce64ed7f3db62ad2ea92968f009013e04;hp=67edb37da53fef7cf3511f07fe8d5fe488b36752;hpb=e8b8c8601ccdc2fdb2093c5228c071d14182004f;p=jalview.git

diff --git a/test/jalview/datamodel/PAEContactMatrixTest.java b/test/jalview/datamodel/PAEContactMatrixTest.java
index 67edb37..fa7aca5 100644
--- a/test/jalview/datamodel/PAEContactMatrixTest.java
+++ b/test/jalview/datamodel/PAEContactMatrixTest.java
@@ -73,7 +73,7 @@ public class PAEContactMatrixTest
     verifyPAEmatrix(seq, aa, 0, 0, 4);
 
     // test clustering
-    paematrix.setGroupSet(GroupSet.makeGroups(paematrix, 0.1f, false));
+    paematrix.setGroupSet(GroupSet.makeGroups(paematrix, false,0.1f, false));
 
     // remap - test the MappableContactMatrix.liftOver method
     SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
@@ -116,7 +116,11 @@ public class PAEContactMatrixTest
     AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
     newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
             null);
-    ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
+    // check for null on out of bounds
+    ContactListI alcl = alForSeq.getContactListFor(newaa, newaa.annotations.length);
+    assertNull(alcl,"Should've gotten null!");
+    // now check for mapping
+    alcl = alForSeq.getContactListFor(newaa, 1);
     assertNotNull(alcl);
     mappedCl = alcl.getMappedPositionsFor(0, 4);
     assertNotNull(mappedCl);