Merge branch 'develop' into patch/JAL-3088_finalbracenotinrightplace

[jalview.git] / test / jalview / datamodel / PAEContactMatrixTest.java

diff --git a/test/jalview/datamodel/PAEContactMatrixTest.java b/test/jalview/datamodel/PAEContactMatrixTest.java
index 67edb37..fa7aca5 100644 (file)
--- 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);